Can I Cite a Preprint in My Research Paper? Complete Guide by Field & Journal (2026)

Yes, you can cite preprints—but whether you should depends on your target journal, your field, and the specific preprint’s status. Since 2020, preprint citation policies have evolved dramatically, yet confusion persists because guidance varies widely across disciplines and publishers.

The COVID-19 pandemic fundamentally changed how the scientific community views preprints. What was once primarily accepted in physics and mathematics has expanded across biology, medicine, and social sciences. However, four years after this shift accelerated, researchers still encounter conflicting advice, outdated policies, and field-specific controversies about preprint citations.

This comprehensive guide explains current preprint citation policies across major journals and fields, when citing preprints strengthens versus weakens your manuscript, how to format preprint citations correctly across different style guides, and what to do when a cited preprint is later retracted, updated, or contradicted by peer review.

In this guide, you’ll learn:

• Current preprint citation policies at major journals (Nature, Science, NEJM, and 50+ others)
• Field-specific norms from physics to medicine
• When citing preprints helps versus hurts your manuscript
• Correct citation formats for all major style guides
• How to handle preprints that are later published, retracted, or contradicted
• Practical decision frameworks for whether to cite specific preprints
• Common mistakes that trigger reviewer concerns

Whether you’re a PhD student navigating your first manuscript submission or an experienced researcher adapting to evolving norms, understanding when and how to cite preprints appropriately has become essential for modern academic publishing.

Quick Answer: Can You Cite Preprints in 2026?

The short answer: Yes, most journals now explicitly allow preprint citations—but with important caveats.

Current Status Across Academia

General acceptance: Approximately 70-80% of journals across all disciplines now permit citing preprints in reference lists, a dramatic increase from about 40-50% in 2019. This shift represents one of the most significant changes in academic publishing norms in recent decades.

Field variation matters enormously:

• Physics, mathematics, computer science: Preprint citations have been standard practice for 30+ years via arXiv
• Biology and life sciences: Rapid acceptance since 2020, bioRxiv citations now mainstream
• Medicine and clinical research: Growing acceptance but with more caution and restrictions
• Social sciences: Increasing acceptance but uneven across subfields
• Humanities: Still developing norms, varies significantly by discipline

Quality and transparency requirements: While journals increasingly accept preprint citations, they universally require:

• Clear indication of preprint status in citations
• Proper repository identification (bioRxiv, arXiv, medRxiv, etc.)
• DOI or permanent identifier when available
• Version number specification for repositories with versioning
• Access dates for transparency

What Changed Since 2020

The COVID-19 pandemic served as an inflection point for preprint acceptance across disciplines:

Institutional changes:

• Web of Science launched the Preprint Citation Index in 2022, legitimizing preprints as citable scholarly outputs
• PubMed began indexing selected preprints from bioRxiv, medRxiv, and Research Square in 2020
• Major funders (NIH, Wellcome, Gates Foundation) explicitly recognized preprints as research outputs
• University promotion and tenure committees increasingly accept preprints in evaluation dossiers

Publisher policy evolution:

• Nature, Science, Cell, and other prestigious journals updated policies to explicitly allow preprint citations
• Most open-access publishers (PLOS, BMC, Frontiers, MDPI) fully embraced preprint citations
• Traditional society journals followed suit, though with varying enthusiasm
• Even conservative medical publishers softened restrictions (with notable exceptions)

Cultural normalization:

• Preprint posting became routine in many fields during COVID-19
• Citation of preprints lost its “controversial” status in most disciplines
• Reviewer complaints about preprint citations decreased significantly
• Editorial policies shifted from “discouraged” to “accepted” or “encouraged.”

What hasn’t changed: Journals still expect proper notation, and reviewers may scrutinize preprint citations more carefully than peer-reviewed sources, particularly for core claims or controversial findings. Understanding when preprint citations strengthen versus weaken your manuscript remains crucial for strategic submission.

Comprehensive Journal Policies on Citing Preprints

Different publishers and journals maintain different policies regarding preprint citations. This table summarizes current policies at major journals as of January 2026, but always verify with the specific journal’s author guidelines as policies continue to evolve.

Major Journal and Publisher Policies

How to Check Your Target Journal’s Policy

Even with this comprehensive table, policies evolve rapidly. Before citing preprints, verify your specific target journal’s current policy:

Step 1: Check author guidelines

• Download the PDF of “Instructions to Authors” or “Author Guidelines”
• Search (Ctrl+F) for “preprint,” “arXiv,” “bioRxiv,” or “citation”
• Look in the “References” or “Citations” section specifically
• Some journals have dedicated “Preprint Policy” sections

Step 2: Examine recent publications

• Browse 10-15 recently published articles in your target journal
• Check their reference lists for preprint citations
• Note how preprints are formatted
• If you find preprint citations in recent articles, the journal clearly accepts them

Step 3: Use policy databases

• Sherpa Romeo (https://v2.sherpa.ac.uk/romeo/) – Publisher policies on preprints
• Transpose (https://transpose-publishing.github.io/) – Comprehensive preprint policies
• ASAPbio Preprint Policy Database – Field-specific guidance

Step 4: Contact the editorial office directly

• Email template: “Does [Journal Name] accept citations of preprints in reference lists? If so, is there a preferred citation format?”
• Most editorial offices respond within 3-7 business days
• Keep their response for your records
• Reference it in your cover letter if relevant

Step 5: When uncertain, acknowledge in your cover letter

• Be proactive: “This manuscript cites [number] preprints from [repositories]. We’ve formatted these according to [style guide]. Please advise if modifications are needed.”
• Shows awareness and professionalism
• Allows editors to provide guidance before peer review
• Demonstrates good faith compliance effort

Understanding how journal editors make decisions can help you anticipate how they might evaluate manuscripts with preprint citations.

When Citing Preprints Strengthens Your Manuscript

Strategic use of preprint citations can actually enhance your manuscript’s credibility and demonstrate your awareness of cutting-edge developments. Here’s when citing preprints works in your favor.

1. The Work Represents Genuinely Cutting-Edge Science

When this applies:

• Published peer-reviewed literature doesn’t yet cover this specific development
• The preprint represents the current frontier of knowledge in your field
• Waiting for a peer-reviewed publication would make your literature review outdated
• The preprint is from established researchers at reputable institutions

Example scenario: You’re writing about CRISPR applications published in late 2025. Several important methodological advances appeared as preprints in December 2025 but won’t be peer-reviewed until mid-2026. Your manuscript submitted in January 2026 would appear less thorough without citing these preprints, as reviewers working in this area will certainly know about them.

Why this strengthens your manuscript:

• Demonstrates comprehensive literature knowledge
• Shows you’re engaged with current research
• Signals you’re part of the active research community
• Reviewers appreciate awareness of recent developments

Best practice: Acknowledge the preprint status in text: “Recent preliminary findings (Author et al., 2025, preprint) suggest…”

2. Building Directly on Very Recent Work

When this applies:

• Your research specifically extends or responds to findings in a recent preprint
• The preprint methodology directly informed your experimental design
• You’re testing predictions made in the preprint
• Time-sensitive fields where waiting for publication isn’t practical

Example scenario: A preprint in computational biology introduced a new algorithm in November 2025. Your research applies and extends this algorithm to a different organism. The preprint won’t be published until summer 2026, but your work builds directly on it. Not citing it would leave reviewers confused about where your methodological foundation came from.

Why this strengthens your manuscript:

• Clearly establishes your research rationale
• Shows logical progression of scientific ideas
• Demonstrates engagement with contemporary research
• Provides the necessary methodological context

Best practice: Include a detailed discussion of how the preprint relates to your work. Consider contacting preprint authors to confirm their findings and potentially coordinate publication timing.

3. Physics, Mathematics, and Computer Science Contexts

When this applies:

• You’re submitting to journals in physics, mathematics, or computer science
• ArXiv has been the standard in your field for decades
• Not citing relevant arXiv preprints would appear outdated
• Conference proceedings and preprints are accepted publication formats

Why arXiv fields different?

• Preprint citation has been standard practice since the 1990s
• Many groundbreaking papers were first (and sometimes only) on arXiv
• The field expects researchers to be monitoring arXiv regularly
• Peer review in these fields often happens informally via preprint comments and citations

Example: In theoretical physics, it’s common to cite arXiv papers that are years old and may never be formally published. The arXiv version is considered the authoritative source. Insisting on peer-reviewed versions only would disconnect you from field norms.

Why this strengthens your manuscript:

• Demonstrates that you follow field conventions
• Shows awareness of relevant work regardless of publication status
• Signals insider knowledge of the research community
• Aligns with reviewer expectations

4. Demonstrating Comprehensive Literature Knowledge

When this applies:

• You’re conducting a thorough literature review
• Recent preprints represent important perspectives on your topic
• Omitting preprints would leave obvious gaps
• Your field values comprehensive citation practices

Example scenario: You’re writing a review article on machine learning applications in drug discovery. Several important methodological innovations appeared as preprints in 2025. While not yet peer-reviewed, omitting them would make your review appear incomplete to specialists in the field.

Why this strengthens your manuscript:

• Shows thoroughness and diligence
• Demonstrates active engagement with current literature
• Signals you’re monitoring multiple channels beyond published journals
• Reviewers appreciate comprehensive coverage

Best practice: Include a methods statement in your review indicating: “We searched published literature and preprints from [repositories] through [date].”

5. Supporting Open Science and Preprint Ecosystems

When this applies:

• Your target journal explicitly supports open science practices
• You’re contributing to normalizing preprint citations
• The journal or field encourages preprint posting
• You want to support researchers who share work openly

Journals particularly receptive to this:

• PLOS journals (explicit open science mission)
• eLife (strong preprint advocacy)
• BMC series (open access philosophy)
• Nature Communications (open access with preprint support)
• Frontiers journals (progressive policies)

Why this strengthens your manuscript:

• Aligns with journal values and editorial philosophy
• Demonstrates commitment to open science principles
• Supports the preprint ecosystem you likely benefit from
• May positively influence editor and reviewer perception

Best practice: Mention in your cover letter if relevant: “This manuscript cites several preprints, reflecting our commitment to engaging with openly shared research and supporting preprint ecosystems.”

6. Discussing the Evolution of Scientific Ideas

When this applies:

• You’re specifically discussing how ideas evolved across preprint and published versions
• The intellectual history of a concept matters to your argument
• Demonstrating scientific process is part of your contribution
• Comparing preliminary vs. conclusions

Example scenario: A hypothesis was first proposed in a 2023 preprint, modified in peer review feedback visible on the preprint server, and published with significant changes in 2024. Your research discusses how the hypothesis evolved, making citations of both versions scientifically valuable.

Why this strengthens your manuscript:

• Demonstrates sophisticated understanding of scientific process
• Provides valuable meta-scientific analysis
• Shows careful attention to intellectual development
• Adds depth to scientific discourse

Best practice: Be explicit about citing different versions: “The initial hypothesis (Author et al., 2023, preprint) differed from the published version (Author et al., 2024) in several key respects…”

When Citing Preprints Weakens Your Manuscript (Or Is Risky)

While preprint citations can strengthen manuscripts in appropriate contexts, they can also undermine credibility or trigger reviewer concerns in specific situations. Understanding when to avoid preprint citations is equally important.

1. Peer-Reviewed Published Version Already Exists

The most common and easily avoided mistake: citing a preprint when the peer-reviewed version is available.

Why this is problematic:

• Appears lazy or careless about the literature review
• Suggests you didn’t check for updates before submission
• May contain outdated information (preprint data might differ from published version)
• Reviewers will immediately notice and may question your thoroughness
• The published version is always more authoritative

How preprints and publications relate:

• Preprints often remain on servers even after journal publication
• DOIs for both versions exist and can both be found in searches
• Authors don’t always link the preprint and published versions
• CrossRef connections are improving, but not universal

How to avoid this mistake:

• Before finalizing your manuscript, search for each preprint author’s name + publication year + key terms
• Check the preprint server page—many now display “Published in [Journal]” banners
• Use CrossRef or PubMed to verify publication status
• Set up alerts for preprints you’re monitoring
• Do a final check during revision stages

Exception: When you’re specifically discussing the preprint version as distinct from the published version (e.g., comparing how findings changed through peer review).

Example of correct dual citation when relevant: “Initial findings (Smith et al., 2024, bioRxiv preprint) suggested X; however, after peer review and additional experiments, the published version (Smith et al., 2025, Nature) concluded Y.”

2. Medical or Clinical Claims with Patient Care Implications

Fields with the highest stakes for accuracy exercise the most caution about preprint citations.

Why medical preprints are riskier:

• Patient safety implications if incorrect information is propagated
• Higher public and media attention to medical research
• Conservative journal cultures (especially NEJM, JAMA)
• History of preprint retractions in COVID-19 research
• Regulatory and liability concerns

Scenarios requiring extra caution:

• Treatment efficacy claims based on unreviewed data
• Drug safety profiles from preprints
• Clinical guidelines built on preprint evidence
• Diagnostic accuracy studies without peer review
• Public health recommendations from preliminary data

Journal-specific considerations:

• NEJM strongly discourages preprint citations for clinical claims
• JAMA prefers peer-reviewed sources for medical evidence
• The Lancet reviews preprint citations case-by-case
• Clinical specialty journals vary in receptiveness

When medical preprint citations might be acceptable:

• Background/context information, not core claims
• Methodological references (analytical techniques, not results)
• Rapidly evolving situations where preprints are the only available source
• Explicitly acknowledged as preliminary evidence

Best practice for medical manuscripts:

• Prioritize peer-reviewed sources for all clinical claims
• If you must cite medical preprints, acknowledge limitations explicitly
• Mention in your cover letter: “We cite one preprint ([citation]) as it represents the only available data on [topic]; we’ve clearly noted its preliminary status.”
• Be prepared to remove or replace if reviewers object

3. Controversial, Disputed, or Retracted Claims

Preprints that have attracted significant criticism or have been retracted pose significant risks to your manuscript’s credibility.

Red flags indicating problematic preprints:

• Multiple critical comments on the preprint server
• PubPeer or other post-publication review sites highlighting concerns
• Authors have posted corrections or withdrawn claims
• Preprint has been retracted (yes, this happens)
• Contradicts well-established evidence without a compelling rationale
• Makes extraordinary claims without extraordinary evidence
• The authors have known credibility issues or a misconduct history

Why does this weaken your manuscript?

• Associating your work with discredited research harms your credibility
• Reviewers may question your critical evaluation skills
• Editors may view it as poor judgment
• If the preprint is later retracted, you’ll need corrections

Example scenarios:

• COVID-19 saw several high-profile preprint retractions (hydroxychloroquine studies, superspreader claims with flawed modeling)
• Social sciences experienced preprint controversies around politically sensitive topics
• The psychology replication crisis highlighted problems with preliminary findings

How to evaluate preprint quality:

• Check for comments and peer reviews on the preprint server
• Search the paper on PubPeer, RetractionWatch, and similar sites
• Look at citation context—how are others citing it?
• Consider author’s track record and institutional affiliation
• Evaluate the methodology critically yourself
• Check if the preprint has been updated with corrections

If you’ve already cited a controversial preprint:

• During revision, you can remove it
• Explain in response to reviewers if they flag it
• Replace with peer-reviewed sources if available

4. Target Journal Explicitly Discourages Preprint Citations

Some journals maintain conservative policies despite broader field trends.

Journals still cautious about preprints:

• New England Journal of Medicine (NEJM) – maintains the strictest policies
• Some traditional society journals in conservative fields
• Certain medical specialty journals
• A few humanities journals are resistant to change

Why journals discourage preprints:

• Disciplinary culture and tradition
• Concerns about quality control
• Editorial board resistance to change
• Field-specific norms (particularly medicine, some humanities)
• Liability or institutional risk concerns

How to identify journal hesitance:

• Author guidelines specifically discourage preprints
• No preprint citations in recently published articles
• Conservative editorial tone about peer review importance
• Society journals with traditional governance structures

What to do if your target journal discourages preprints:

• Respect their policy—replace preprint citations with peer-reviewed sources
• If genuinely no alternative exists, mention in the cover letter and ask for guidance
• Consider whether this journal is the right fit for your work
• Find journals with more progressive policies if preprint citations are important

Strategic consideration:

• Some researchers post their own work as preprints but avoid citing others’ preprints in manuscripts to conservative journals
• This maintains the benefits of preprint sharing while avoiding citation policy conflicts

5. Low-Quality or Questionable Preprint Sources

Not all preprint servers maintain equivalent quality standards or legitimacy.

Reputable, established preprint servers:

• arXiv – Physics, mathematics, CS, quantitative biology (established 1991)
• bioRxiv – Biology and life sciences (established 2013)
• medRxiv – Medical and health sciences (established 2019)
• ChemRxiv – Chemistry (established 2017)
• PsyArXiv – Psychology (established 2016)
• SocArXiv – Social sciences (established 2016)
• SSRN – Social sciences, economics, law (established 1994)
• Research Square – Multidisciplinary (established 2018)

Red flags indicating questionable preprint servers:

• Server launched very recently without institutional backing
• No clear moderation or screening processes
• Accepts preprints in unrelated fields (supposed physics server accepting medical papers)
• Unclear ownership or governance
• Predatory publisher connections
• No DOI assignment or persistent identifiers
• Poor technical infrastructure or security

Screening processes matter:

• Reputable servers conduct basic screening (plagiarism checks, obvious pseudoscience filtering)
• They don’t conduct peer review, but do prevent completely inappropriate content
• Quality varies even on reputable servers, but minimum standards exist

How to verify preprint server legitimacy:

• Check if it’s operated by a reputable non-profit or university consortium
• Look for an editorial board or advisory board with recognized scientists
• Verify it’s indexed by CrossRef and assigns DOIs
• See if it’s integrated with journal submission systems
• Check if major funders recognize it (NIH, Wellcome, etc.)

If you encounter a preprint from a questionable source:

• Verify the research through other means
• Check if authors have credible institutional affiliations
• Search for the work in reputable preprint servers or journals
• Consider not citing it if credibility is uncertain

6. Building Core Arguments Entirely on Unreviewed Work

Using preprints as supplementary evidence is one thing; building your entire argument on them is another.

The problem with preprint-dependent arguments:

• Peer review might reveal flaws in the foundation of your work
• Reviewers will question the stability of your theoretical or empirical basis
• If preprints are contradicted, your entire argument collapses
• Demonstrates over-reliance on preliminary findings

Scenarios where this becomes problematic:

• Your hypothesis rests entirely on findings from 3-4 preprints
• Your methodology is justified solely by preprint evidence
• Core theoretical frameworks are only described in preprints
• Key data supporting your interpretation comes only from unreviewed sources

How reviewers respond:

• “The authors build their argument on preliminary findings that haven’t been peer-reviewed…”
• “The theoretical foundation requires validation through peer-reviewed publication before…”
• “Given the reliance on preprints for core claims, I recommend waiting for peer review of these sources…”

Best practices:

• Use preprints to supplement peer-reviewed evidence, not replace it
• If your field is emerging and preprints dominate, acknowledge this explicitly
• Balance preprint citations with established literature
• Frame preprint-based claims carefully: “Preliminary evidence suggests…” rather than “Research demonstrates…”

Strategic revision approach:

• If reviewers flag over-reliance on preprints, consider:
  • Waiting for some preprints to be published before resubmitting
  • Finding peer-reviewed alternatives that support similar points
  • Reframing claims as more tentative given preliminary evidence
  • Adding sections that don’t depend on preprint findings

Understanding how to respond to reviewer comments about preprint citations can help you address concerns effectively.

How to Cite Preprints Correctly: Format Guide for All Major Styles

Proper preprint citation format varies across style guides, but all share common requirements: clear indication of preprint status, repository identification, and permanent identifiers. Here’s comprehensive guidance for major citation styles.

Universal Preprint Citation Principles

Regardless of style guide, always include:

1. Preprint status indication – Use “[Preprint]” notation, “Preprint,” or style-specific designation
2. Repository name – bioRxiv, arXiv, medRxiv, ChemRxiv, etc.
3. DOI when available – Provides a permanent link and enables tracking
4. Version number if applicable – Many repositories allow multiple versions
5. Access date for transparency – Some styles require, others recommend
6. Authors and title – Standard bibliographic information

Additional best practices:

• Link DOIs properly using the https://doi.org/ format
• Check for updated versions before final submission
• Verify DOI links work correctly
• Include the year of preprint posting
• Note if discussing a specific version vs. the most current

APA 7th Edition (Psychology, Education, Social Sciences)

General format:

Author, A. A., & Author, B. B. (Year). Title of preprint. Repository Name. https://doi.org/xxxxx

Example:

Smith, J. K., & Jones, M. L. (2025). Neural mechanisms underlying decision-making in uncertain environments. bioRxiv. https://doi.org/10.1101/2025.01.15.123456

With version number:

Author, A. A. (Year). Title of preprint (Version 2). Repository Name. https://doi.org/xxxxx

In-text citation:

(Smith & Jones, 2025)
or
Smith and Jones (2025) found...

Special considerations:

• APA 7th edition added explicit preprint guidance in 2020
• The repository name is treated like a publisher
• No “[Preprint]” notation required in reference list (context is clear)
• Mention preprint status in text if needed: “preliminary findings (Smith & Jones, 2025, preprint)…”

Access date (optional but recommended for transparency):

Smith, J. K., & Jones, M. L. (2025). Neural mechanisms underlying decision-making in uncertain environments. bioRxiv. Retrieved January 20, 2026, from https://doi.org/10.1101/2025.01.15.123456

NLM/PubMed Style (Medical and Health Sciences)

General format:

Author AA, Author BB. Title of preprint. Repository [Preprint]. Year Month Day [cited Year Month Day]. Available from: https://doi.org/xxxxx

Example:

Smith JK, Jones ML. Neural mechanisms underlying decision-making in uncertain environments. bioRxiv [Preprint]. 2025 Jan 15 [cited 2026 Jan 20]. Available from: https://doi.org/10.1101/2025.01.15.123456

With version:

Smith JK, Jones ML. Neural mechanisms underlying decision-making in uncertain environments. Version 2. bioRxiv [Preprint]. 2025 Jan 15 [updated 2025 Feb 10; cited 2026 Jan 20]. Available from: https://doi.org/10.1101/2025.01.15.123456

In-text citation:

(Smith and Jones, 2025)
or
Smith and Jones (2025) demonstrated...

Special considerations:

• NLM style explicitly includes “[Preprint]” notation
• Citation date is required (when you accessed it)
• Useful for the rapidly changing preprint landscape
• Update dates matter if the preprint was revised

Chicago Style (Humanities, Some Social Sciences)

Notes-Bibliography format:

Footnote:

1. John K. Smith and Mary L. Jones, "Neural Mechanisms Underlying Decision-Making in Uncertain Environments," bioRxiv, January 15, 2025, preprint, https://doi.org/10.1101/2025.01.15.123456.

Bibliography entry:

Smith, John K., and Mary L. Jones. "Neural Mechanisms Underlying Decision-Making in Uncertain Environments." bioRxiv, January 15, 2025. Preprint. https://doi.org/10.1101/2025.01.15.123456.

Author-Date format:

Reference list:

Smith, John K., and Mary L. Jones. 2025. "Neural Mechanisms Underlying Decision-Making in Uncertain Environments." bioRxiv. Preprint. https://doi.org/10.1101/2025.01.15.123456.

In-text citation:

(Smith and Jones 2025)

Special considerations:

• Chicago offers flexibility in preprint notation placement
• “Preprint” can appear before or after the repository name
• DOI should be formatted as a full URL
• Accessed date is optional unless the content might change

IEEE Style (Engineering, Computer Science, Technology)

General format:

[1] A. Author and B. Author, "Title of preprint," Repository, preprint, Year. [Online]. Available: https://doi.org/xxxxx

Example:

[1] J. K. Smith and M. L. Jones, "Neural mechanisms underlying decision-making in uncertain environments," bioRxiv, preprint, 2025. [Online]. Available: https://doi.org/10.1101/2025.01.15.123456

With version and accessed date:

[1] J. K. Smith and M. L. Jones, "Neural mechanisms underlying decision-making in uncertain environments," version 2, bioRxiv, preprint, 2025. [Online]. Available: https://doi.org/10.1101/2025.01.15.123456. [Accessed: Jan. 20, 2026].

In-text citation:

Smith and Jones [1] demonstrated...
or
Recent work [1] has shown...

Special considerations:

• IEEE uses numbered citations
• “Preprint” designation is standard
• [Online] and Available: format is characteristic of IEEE
• Accessed date in brackets at the end if included

ACS Style (Chemistry)

General format:

Author, A.; Author, B. Title of Preprint. Repository [Online] Year. https://doi.org/xxxxx (accessed Month Day, Year).

Example:

Smith, J. K.; Jones, M. L. Neural Mechanisms Underlying Decision-Making in Uncertain Environments. bioRxiv [Online] 2025. https://doi.org/10.1101/2025.01.15.123456 (accessed Jan 20, 2026).

With version:

Smith, J. K.; Jones, M. L. Neural Mechanisms Underlying Decision-Making in Uncertain Environments, version 2. bioRxiv [Online] 2025. https://doi.org/10.1101/2025.01.15.123456 (accessed Jan 20, 2026).

In-text citation (superscript):

Recent findings^1^ suggest...

In-text citation (author-date variant):

(Smith and Jones, 2025)

Special considerations:

• ACS uses the [Online] designation for electronic sources
• Accessed date is required in parentheses
• Semicolons between authors (not commas or “and”)
• ChemRxiv is the natural repository for chemistry preprints

MLA 9th Edition (Humanities, Literature)

General format:

Author, First Name. "Title of Preprint." Repository, Day Month Year, DOI or URL. Preprint.

Example:

Smith, John K., and Mary L. Jones. "Neural Mechanisms Underlying Decision-Making in Uncertain Environments." bioRxiv, 15 Jan. 2025, https://doi.org/10.1101/2025.01.15.123456. Preprint.

With version:

Smith, John K., and Mary L. Jones. "Neural Mechanisms Underlying Decision-Making in Uncertain Environments." Version 2, bioRxiv, 15 Jan. 2025, updated 10 Feb. 2025, https://doi.org/10.1101/2025.01.15.123456. Preprint.

In-text citation:

(Smith and Jones)
or
Smith and Jones argue that...

Special considerations:

• MLA places “Preprint” at the end as a descriptor
• Day-Month-Year format (European style)
• Accessed date is optional for stable content

• Full URL or DOI acceptable

Vancouver Style (Medical and Biomedical Sciences)

General format (very similar to NLM):

Author AA, Author BB. Title of preprint [Preprint]. Repository: Year Month Day. Available from: https://doi.org/xxxxx

Example:

Smith JK, Jones ML. Neural mechanisms underlying decision-making in uncertain environments [Preprint]. bioRxiv: 2025 Jan 15. Available from: https://doi.org/10.1101/2025.01.15.123456

In-text citation (numbered):

Recent research (1) has demonstrated...
or
Smith and Jones (1) found...

Special considerations:

• Vancouver uses numbered citations like IEEE
• [Preprint] notation immediately after title
• Colon after repository name
• Common in medical journals

Harvard Style (Business, Social Sciences in the UK/Australia)

General format:

Author, A.A. and Author, B.B. (Year) 'Title of preprint', Repository, preprint. Available at: https://doi.org/xxxxx (Accessed: Day Month Year).

Example:

Smith, J.K. and Jones, M.L. (2025) 'Neural mechanisms underlying decision-making in uncertain environments', bioRxiv, preprint. Available at: https://doi.org/10.1101/2025.01.15.123456 (Accessed: 20 January 2026).

In-text citation:

(Smith and Jones, 2025)
or
Smith and Jones (2025) demonstrated...

Special considerations:

• Single quotes around title (UK convention)
• “Available at:” before DOI
• Accessed date with full month name
• Common in UK universities

In-Text Citation Best Practices Across All Styles

Indicating preprint status in your writing:

When to mention preprint status explicitly:

• First mention of a preprint citation
• Core claims based on preprint evidence
• Medical or clinical findings from preprints
• Recent work that readers might not be familiar with

How to indicate preprint status naturally:

✅ Good examples:

• “Preliminary findings (Smith et al., 2025, bioRxiv preprint) suggest…”
• “Recent unreviewed work by Jones and colleagues (2025, preprint) demonstrated…”
• “Smith et al. (2025) reported in a bioRxiv preprint that…”
• “According to preprint data (Author et al., 2025)…”

❌ Avoid these constructions:

• “The unpublished study by Smith…” (sounds dismissive)
• “Although not peer-reviewed, Smith found…” (unnecessarily defensive)
• Citing preprints without any status indication (leaves readers uncertain)

Hedging appropriately:

• Use slightly more tentative language for preprint-based claims
• “Recent preliminary data suggest…” rather than “Research proves…”
• “Initial findings indicate…” rather than “Studies definitively show…”
• This protects your argument if preprint findings change through peer review

Balancing transparency with flow:

• You don’t need to say “preprint” every single time you cite the same work
• Indicate status at first mention, then cite normally
• Readers will remember from the reference list

Field-Specific Norms and Cultural Expectations

Different academic disciplines have developed distinct cultures around preprint citation, shaped by historical practices, publication timelines, and field-specific values. Understanding your field’s norms is essential for strategic manuscript preparation.

Physics and Astronomy: The Original Preprint Culture

Historical context:

• arXiv launched in 1991 (originally as xxx.lanl.gov)
• Preprint culture existed even before digital archives
• Physicists shared preprints via mail for decades

Current practice:

• arXiv citations are completely standard and expected
• Often cited even when a published journal version exists
• Not citing relevant arXiv papers makes you appear unaware of current research
• Many groundbreaking papers exist only on arXiv
• Preprint posting is routine, not controversial

Citation norms:

• Mix of arXiv and journal citations in reference lists is universal
• arXiv numbers (e.g., arXiv:2501.12345) commonly appear
• Published versions may include “Also available as arXiv:XXXX.”
• Reviewers expect comprehensive arXiv awareness

Why physics embraced preprints:

• Rapid communication is essential for a competitive field
• Long journal publication timelines (6-12 months)
• Strong culture of open sharing
• Conference proceedings insufficient for detailed work
• Mathematics-heavy content is less subject to misinterpretation concerns

Practical implications:

• If you’re submitting to physics journals, extensive arXiv citations are normal
• Reviewers will notice if you’ve missed key arXiv papers
• The arXiv version is often considered authoritative
• Some papers circulate for years on arXiv before (or without) formal publication

Mathematics and Computer Science: Following Physics’ Lead

Disciplinary practices:

• arXiv adoption followed physics (math started in 1998, CS in the early 2000s)
• Conference preprints/proceedings are common in CS
• Mathematics has a longer acceptance of non-journal publications
• Theoretical CS is closer to math norms; applied CS varies

Citation culture:

• arXiv citations standard in pure mathematics
• Computer science conferences are peer-reviewed and citable
• Conference proceedings are often posted as preprints
• Technical reports and working papers have a long tradition

Subfield variation:

• Theoretical CS and math: High arXiv acceptance
• Applied CS and engineering: More traditional journal focus
• Machine learning/AI: Rapidly adopting preprint culture (ICLR, NeurIPS proceedings on arXiv)
• Software engineering: More conservative

Why these fields embrace preprints:

• Proof-based work is verifiable by readers
• Ideas matter more than experimental validation
• Competition for priority is intense
• Traditional publication can take 12-24 months
• Strong open-source software culture aligns with open preprints

Biology and Life Sciences: Rapid Evolution Since 2020

Pre-COVID status (before 2020):

• bioRxiv was launched in 2013, but adoption was slow
• Many researchers are hesitant about preprint posting
• Citation of bioRxiv was uncommon and sometimes discouraged
• Generational divide (younger researchers are more supportive)

COVID-19 transformation:

• bioRxiv submissions exploded during the pandemic
• Rapid communication became essential for public health
• Journals’ relaxed policies to accommodate urgent research
• Media and policy attention legitimized preprints
• Funding agencies endorsed preprints as research outputs

Current status (2026):

• bioRxiv citations now mainstream in most subfields
• Most biology journals explicitly accept preprint citations
• Preprint posting routine for competitive labs
• Still more conservative than physics but rapidly normalizing

Subfield variation:

• Molecular biology, genetics, genomics: High preprint acceptance
• Ecology, evolution: Growing but uneven adoption
• Neuroscience: Strong preprint culture
• Cell biology: Increasingly common
• Structural biology: Methods preprints are very common
• Clinical research: More cautious (see medicine section)

Citation considerations:

• Check whether the published version exists (common lag: 6-12 months)
• bioRxiv citations are widely accepted but indicate status
• Some labs post everything to bioRxiv; others are selective
• Version numbers matter (methodology might change between v1 and v3)

Medicine and Clinical Research: Cautious Acceptance

Why is medicine conservative?

• Patient safety implications of wrong information
• Media attention amplifies errors
• Regulatory scrutiny (FDA, EMA rely on peer-reviewed data)
• Liability concerns
• History of retracted preprints during COVID-19
• Conservative professional culture

Current policies:

• medRxiv is accepted but more scrutinized than bioRxiv
• Explicit notation of preprint status required
• Some top journals (NEJM) maintain restrictions
• Clinical journals vary widely in acceptance
• Preference for peer-reviewed sources when available

NEJM’s Ingelfinger Rule:

• Won’t publish articles previously posted as preprints (with some COVID exceptions)
• Can cite others’ preprints,, but with caution
• Among the strictest policies in academic publishing
• Named after former editor Franz Ingelfinger

Other medical journal approaches:

• JAMA: Allows preprint citations but discourages over-reliance
• The Lancet: Accepts preprints, reviews carefully
• BMJ: Supportive but emphasizes critical evaluation
• PLOS Medicine: Fully accepts preprints
• Specialty journals: Highly variable

Types of medical preprints:

• Methodological papers: More accepted (analytical techniques, study protocols)
• Epidemiological data: Accepted with notation
• Clinical trials: More scrutiny
• Treatment efficacy: Highest skepticism
• Diagnostic studies: Case-by-case

Best practices for medical manuscripts:

• Prioritize peer-reviewed sources for all clinical claims
• Use preprints for methodological citations or very recent developments
• Clearly indicate limitations of preprint evidence
• Be prepared to justify preprint citations to reviewers
• Update to published versions during revision if possible

Social Sciences: Uneven but Growing Adoption

Historical context:

• Economics had a working paper culture (NBER, SSRN since the 1990s.
• Other social sciences slower to adopt
• Cultural resistance in some subfields
• Younger scholars are more supportive

Current landscape:

Economics:

• SSRN and NBER working papers standard for decades
• Citations of working papers are completely normal
• Many important papers exist only as working papers
• Journal publication can lag years behind working paper circulation

Political Science:

• Growing preprint acceptance via SocArXiv
• Working papers common
• Some top journals are now supportive
• Generational and methodological divides

Sociology:

• SocArXiv launched in 2016
• Adoption slower than economics
• Theoretical work is more resistant than quantitative work
• Increasing acceptance among younger scholars

Psychology:

• PsyArXiv rapidly growing
• The replication crisis increased openness to transparency
• Cognitive/experimental psychology is more accepting than clinical psychology
• Registered reports complementing preprints

Anthropology, History, other humanities-adjacent fields:

• Limited preprint adoption
• Book manuscript culture doesn’t align with preprints
• Slower publication timelines make preprints less urgent
• Emerging use for article-length work

Citation norms:

• Economics: Extensive working paper citations expected
• Psychology: Increasingly normal, indicates status
• Sociology/Political Science: Growing, but check journal norms
• Qualitative research: Less preprint infrastructure

Humanities: Limited but Emerging Use

Why humanities lag in preprint adoption:

• Book-based publication culture (not article-focused)
• Longer-form arguments don’t fit the preprint format
• Less time-sensitive than the sciences
• Smaller, slower-moving scholarly conversations
• Concerns about scooping are different
• Some fields value “finished” polished prose

Emerging humanities preprint infrastructure:

• Humanities Commons (general platform)
• PhilPapers (philosophy)
• Field-specific repositories developing
• University repositories hosting working papers

Limited citation of humanities preprints:

• Working paper culture exists, but informal
• Conference papers are shared but rarely cited formally
• Book chapters circulated but not formally citable
• Some journal articles are posted on personal websites or Academia.edu

Subfield variation:

• Digital humanities: More open to preprints
• Philosophy: Some preprint culture via PhilPapers
• History: Very limited
• Literature: Minimal
• Linguistics: Some computational linguistics preprints

Practical guidance for humanities scholars:

• Preprint posting is uncommon but not prohibited
• Citation of preprints is very rare in traditional journals
• May be more accepted in interdisciplinary or digital humanities journals
• Check your specific subfield norms

Chemistry: Growing Infrastructure

chemRxiv status:

• Launched in 2017 (relatively recent)
• Adoption growing but uneven across chemistry subfields
• ACS journals are generally supportive
• Organic synthesis is more accepting than others

Citation practices:

• chemRxiv citations increasingly appear in ACS journals
• Still less common than bioRxiv in biology
• Check specific journal policies
• arXiv chemistry section exists, but is less used than chemRxiv

Why was chemistry slower to adopt?

• Intellectual property concerns (patents)
• Industrial research considerations
• Different publication culture than biology or physics
• Smaller perceived urgency

Current trends:

• Growing acceptance, especially for methods and computational work
• Younger researchers are more supportive
• Integration with journal submission systems is increasing

Practical Decision Tree: Should I Cite This Specific Preprint?

When you encounter a relevant preprint during literature review, use this decision framework to determine whether citing it strengthens or weakens your manuscript.

Decision Flow Chart

START: I found a relevant preprint

STEP 1: Is there a peer-reviewed published version of this work?

• YES → Always cite the published version instead. The only exception is if you’re specifically discussing how the work evolved from preprint to publication. Move to END.
• NO → Continue to STEP 2

STEP 2: What field am I in, and what are preprint norms?

• Physics, Mathematics, or Computer Science → Preprints are standard. Continue to STEP 3.
• Biology or Life Sciences → Generally accepted now. Continue to STEP 3.
• Medicine or Clinical Research → Use caution. Continue to STEP 3 with extra scrutiny.
• Social Sciences → Varies by subfield. Economics/Psychology is more accepting; check the specific journal. Continue to STEP 3.
• Humanities → Rare. Consider whether citation is essential. Continue to STEP 3.

STEP 3: Is this claim medical/clinical with potential patient care implications?

• YES → Exercise extreme caution. Check the target journal policy explicitly. If the journal discourages medical preprint citations, find alternative sources. If the preprint is truly the only source and essential, acknowledge its preliminary status explicitly and be prepared to justify to reviewers. Continue to STEP 4.
• NO → Continue to STEP 4.

STEP 4: Is the preprint from a reputable, established repository?

Reputable repositories:

• arXiv
• bioRxiv
• medRxiv
• chemRxiv
• PsyArXiv
• SocArXiv
• SSRN
• Research Square
• YES (reputable repository) → Continue to STEP 5.
• NO or UNCERTAIN → Research the repository. If it’s questionable or unknown, consider not citing. If you must cite, verify author’s credibility carefully. Continue to STEP 5.

STEP 5: Who are the authors, and what are their credentials?

Check:

• Are they at recognized research institutions?
• Do they have publication track records in this area?
• Are they established or completely unknown?
• Established researchers at reputable institutions → Continue to STEP 6.
• Unknown authors or questionable affiliations → Verify quality extra carefully. Check for red flags. Consider whether citation is necessary. Continue to STEP 6.

STEP 6: Does your target journal allow preprint citations?

How to verify:

• Check author guidelines
• Examine the recently published articles’ reference lists
• Use policy databases (Sherpa Romeo, Transpose)
• Email the editorial office if uncertain
• YES, journal explicitly allows preprints → Continue to STEP 7.
• NO, journal discourages or prohibits preprints → Don’t cite. Find alternative peer-reviewed sources or reconsider journal choice. Move to END.
• UNCLEAR policy → Email editorial office for clarification. If no response, proceed with caution and mention in the cover letter. Continue to STEP 7.

STEP 7: Is this preprint central to your core argument, or is it supplementary evidence?

• CORE CLAIM – Your hypothesis, main methodology, or primary findings depend on this preprint → Reconsider. Building core arguments on unreviewed work is risky. Can you find peer-reviewed alternatives? Can you frame the claim more tentatively? If the preprint is truly essential and irreplaceable, proceed but acknowledge the preliminary nature explicitly. Continue to STEP 8.
• SUPPLEMENTARY EVIDENCE – Supporting detail, methodological reference, or contextual information → Generally OK to cite. Continue to STEP 8.

STEP 8: Have you checked for criticism, corrections, or retractions of this preprint?

Where to check:

• Comments section on the preprint server itself
• PubPeer
• RetractionWatch
• Google Scholar alerts for the title
• Social media discussions (Twitter/X, especially in science communities)
• NO CONCERNS FOUND – Clean preprint with no major criticisms → Continue to STEP 9.
• CRITICISMS OR CONCERNS EXIST – Significant methodological critiques, disputed claims, or corrections posted → Reconsider citing. If the criticism is minor or addressed in later versions, may be OK. If substantial concerns exist, find alternative sources. Continue to STEP 9.
• PREPRINT HAS BEEN RETRACTED → Do not cite. Find alternative sources. Move to END.

STEP 9: Is this the most current version of the preprint?

Check:

• Preprint servers often allow authors to post updated versions
• Version number is usually displayed (v1, v2, v3, etc.)
• Check posting date vs. access date
• YES, citing the most current version → Continue to STEP 10.
• NO, newer version exists → Update your citation to the most recent version unless you’re specifically discussing how findings evolved across versions. Continue to STEP 10.

STEP 10: Final quality assessment – Would I bet my manuscript’s credibility on this preprint?

Consider:

• Does the methodology appear sound?
• Are claims proportionate to evidence?
• Does it align with or contradict established knowledge?
• Would reviewers familiar with this topic view this citation positively or negatively?
• YES, I’m confident in this preprint’s quality and its value to my manuscript → PROCEED WITH CITATION. Format according to your style guide with proper “[Preprint]” notation. Consider mentioning preprint status in text, especially for the first mention or core claims. Move to END.
• NO, I have concerns about quality or appropriateness → Don’t cite. Find peer-reviewed alternatives or omit if not essential. Better to have gaps than questionable citations. Move to END.

END: Citation Decision Made

If citing the preprint:

• ✅ Use proper format with “[Preprint]” notation
• ✅ Include DOI and repository name
• ✅ Cite specific version number
• ✅ Indicate preprint status in text where appropriate
• ✅ Set a reminder to check if it’s been published before your manuscript goes to press
• ✅ Mention in cover letter if preprint citations are unusual for your field or journal

If not citing:

• ✅ Note the preprint for your own knowledge
• ✅ Set up an alert for when/if it’s peer-reviewed and published
• ✅ Find peer-reviewed alternatives that address similar topics
• ✅ If truly no alternatives exist, consider whether your manuscript timing is appropriate

What to Do When a Cited Preprint Gets Published

One of the most common questions about preprint citations: What happens when the preprint you cited is subsequently published in a peer-reviewed journal? The answer depends on timing and your manuscript’s stage in the publication process.

Before You Submit Your Manuscript

Best practice: Always check for published versions immediately before submission.

Search strategy:

1. Google Scholar search for authors + key terms + year
2. Check the preprint server page (many now display “Published in [Journal]” notices)
3. PubMed search if biomedical topic
4. CrossRef or DOI search
5. Check authors’ personal websites or institutional pages

Why this matters:

• Reviewers will notice if you cited a preprint when the published version exists
• Appears careless or suggests outdated literature search
• The published version is always more authoritative
• Methodology or conclusions might have changed through peer review

Action: Update to the published version before submitting. This strengthens your manuscript and demonstrates thoroughness.

Timeline consideration:

• Preprints typically take 6-18 months to publish after posting
• Some fields are faster (bioRxiv to publication often 6-9 months)
• Others are slower (can be 12-24 months in some disciplines)
• COVID-era publications were unusually fast (sometimes 1-3 months)

During Peer Review (Before Your Revision)

If you discover the published version during peer review:

Scenario 1: Reviewers haven’t mentioned it

• Update the citation in your revision
• Mention in your response to reviewers: “We have updated citation [X] to the published version that appeared during review.”
• Shows diligence and awareness
• Reviewers appreciate proactive updates

Scenario 2: Reviewers flagged it

• Thank them for pointing it out
• Update to published version
• Response example: “Thank you for noting that Reference [X] has now been published. We have updated the citation to the peer-reviewed version (Author et al., 2026, Journal Name).”

If findings changed between preprint and publication:

Minor changes:

• Simply update the citation
• No need to revise your text unless the change affects your argument

Significant changes:

• Update citation AND revise relevant text
• Acknowledge if your interpretation needs adjustment
• Example response: “The published version (Author et al., 2026) includes additional experiments not in the preprint. We have revised our discussion in lines XX-XX to reflect these updated findings.”
• Shows scientific integrity

If contradicted by peer review:

• Remove or significantly qualify your reliance on that work
• Example response: “While the preprint (Author et al., 2025) suggested X, peer review revealed methodological concerns, and the published version (Author et al., 2026) now reports Y. We have revised our interpretation accordingly (lines XX-XX).”
• Reviewers will respect honest handling of evolving evidence

After Acceptance But Before Publication

Can you still update citations?

Yes, usually—during different production stages:

Proof stage (copyediting):

• Most journals allow citation updates during proofs
• Notify your production editor
• Provide a complete updated citation
• May incur delays, but usually manageable

Page proof stage:

• More difficult but sometimes possible
• Contact the production editor immediately
• Some journals charge fees for changes at this stage
• Critical citations worth the effort

After final publication (your article is online):

• Too late for normal updates
• If critical to your argument, consider:
  • Correction/erratum (rare for citation updates alone)
  • Note in the online supplementary materials (some journals allow)
  • Update your personal copy/preprint version
  • Mention in future work

How to communicate with production staff:

Email template:

Subject: Citation Update Request - Manuscript [ID]

Dear [Production Editor],

During the production of our manuscript "[Title]" (ID: XXXX), we discovered that Reference [Number], which was cited as a preprint, has now been published in a peer-reviewed journal.

Original citation (preprint):
[Full preprint citation]

Updated citation (published):
[Full published journal citation]

Could this citation be updated in our manuscript? We understand this may cause slight delays and are happy to review updated proofs.

Thank you for your assistance.

When to prioritize updating:

• Core claims depend on this citation
• Published version differs significantly from preprint
• High-impact citation central to your argument
• Field norms strongly prefer peer-reviewed sources

When it’s less critical:

• Background or contextual citation
• Published version identical to preprint
• Dozens of references make small updates less noticeable
• Production timeline constraints

Creating a Dual Citation (When Appropriate)

Sometimes citing both versions provides valuable context:

When to use dual citation:

• Discussing how findings evolved through peer review
• Meta-scientific analysis of the publication process
• Preprint generated significant discussion before publication
• Published version differs substantially from preprint
• You’re studying preprint culture itself

Format examples:

Inline discussion:

"Initial findings (Smith et al., 2024, bioRxiv preprint) suggested that X; however, after peer review and additional experiments, the published version (Smith et al., 2025, Nature) concluded Y, demonstrating how the peer review process refined the original hypothesis."

Reference list: Both citations appear:

Smith, J., Jones, M., & Brown, K. (2024). Title of work. bioRxiv. https://doi.org/10.1101/2024.XX.XX
Smith, J., Jones, M., & Brown, K. (2025). Title of work. Nature, 612, 123-130. https://doi.org/10.1038/sXXXXX

When NOT to dual cite:

• The versions are essentially identical
• You’re not discussing the evolution of ideas
• Space constraints in the reference list
• It appears to inflate citation count artificially

Setting Up Alerts for Preprint Publication

Proactive monitoring prevents outdated citations:

Google Scholar Alerts:

1. Search for the preprint title
2. Click “Create alert” at the bottom of the results
3. Receive email when new citations appear (often includes publication notices)

ResearchGate/Academia.edu:

• Follow authors
• Receive notifications when they post new publications
• Many researchers update their profiles when preprints are published

ORCID monitoring:

• If authors have ORCID profiles, publications automatically appear
• Some services monitor ORCID for updates

Preprint server features:

• Some servers email when preprints you’ve viewed are updated or published
• bioRxiv and medRxiv are improving this functionality
• CrossRef links are becoming more reliable

Manual checking schedule:

• Before final submission: Check all preprints one last time
• During revision: Check again (months may have passed)
• At proof stage: Final check before publication

Automation tools:

• Zotero and Mendeley can sometimes auto-detect published versions
• Still requires manual verification
• Don’t rely entirely on automation

Why Publishers Should but Don’t Always Link Versions

The ideal system:

• Preprint servers and journals would automatically link versions
• DOIs would cross-reference
• Citation databases would merge duplicate entries
• Readers could easily find the peer-reviewed version

Current reality:

• Linking is improving, but inconsistent
• Depends on the authors updating the preprint pages
• Relies on publishers communicating with preprint servers
• CrossRef Event Data helps, but isn’t universal

What you can do:

• When your work is published, update the preprint server page
• Indicate “This preprint has been published in [Journal].”
• Add DOI cross-link
• Helps future researchers cite your work
• Contributes to improving the system

Handling Retracted or Contradicted Preprints

While less common than in peer-reviewed literature, preprint retractions do occur, and preprint findings are sometimes contradicted by subsequent research. Knowing how to handle these situations protects your manuscript’s credibility.

Preprint Retractions: What They Are and Why They Happen

What is preprint retraction?

Unlike journal articles, preprints don’t undergo formal retraction processes in most repositories. Instead:

• Authors can withdraw preprints
• Servers can remove preprints violating policies
• “Retraction” notices may be posted
• The preprint remains accessible but flagged

Common reasons for preprint retraction:

Errors discovered by authors:

• Coding bugs affecting results
• Statistical errors
• Misinterpretation of data
• Failed replication attempts by the same lab

Methodological problems:

• Ethical issues discovered
• Consent problems
• Fabricated or manipulated data
• Plagiarism

Legal or confidentiality issues:

• Patient privacy violations
• Intellectual property disputes
• Legal threats or injunctions

Scientific community concerns:

• Post-publication peer review identifying fatal flaws
• Inability to replicate key findings
• Retraction of underlying data or studies
• Serious criticism from experts

Notable examples from the COVID-19 era:

• Hydroxychloroquine studies with flawed data
• Superspreader event models with coding errors
• Vaccine misinformation preprints
• Epidemiological models with incorrect assumptions

If You’ve Already Cited a Retracted Preprint

Discovery timing affects your options:

During manuscript preparation (before submission):

• Action: Remove the citation entirely
• Replace with peer-reviewed alternative if available
• If no alternative exists and the point was minor, simply omit
• If the point was central, reconsider your argument’s foundation

During peer review (before revision deadline):

• Action: Remove or replace in your revision
• Explicitly mention in response to reviewers (even if they didn’t flag it)
• Example: “We have removed Reference [X] as the preprint was retracted during review due to methodological concerns. We’ve replaced it with [alternative citation].”
• Shows integrity and awareness

After acceptance but before publication:

• Action: Contact editors immediately
• Request citation removal/replacement
• Most journals will accommodate this during production
• Better to cause minor delays than publish citing retracted work

After your article is published:

• Action depends on centrality:

If the retracted preprint was central to your argument:

• Contact journal editors about a formal correction or erratum
• May need to issue a corrigendum explaining the issue
• Example statement: “Reference [X] cited in our article has been retracted. Our conclusions in Section [Y] should be interpreted with caution. Alternative evidence from [new source] suggests…”

If it was minor/contextual:

• May not require formal correction
• Update your personal records
• Note in any follow-up publications
• Respond to inquiries if they arise

If discovery happens years later:

• Less urgent unless people are citing your work specifically for that point
• Consider noting in future publications
• Update personal/lab copies of the manuscript

Preprints Contradicted by Subsequent Research

More common than retraction: preprint findings don’t hold up in peer review or are contradicted by other research.

Types of contradiction:

Major finding doesn’t replicate:

• Original preprint: “Treatment X reduces Disease Y by 50%.”
• Peer-reviewed version: “Treatment X shows no significant effect.”
• Or subsequent studies contradict the finding

Methodology revised, conclusions changed:

• Preprint used Method A, found Result X
• Peer review identified problems with Method A
• Published version used Method B, found Result Y

Effect size is dramatically different:

• The preprint claimed a large effect
• Peer review or replication found a small or no effect
• Your argument may have overstated the evidence

Interpretation disputed:

• Data might be solid, but interpretation contested
• Field consensus moves away from preprint interpretation

How to Handle Contradictions

If discovered before submission:

• Update your framing to acknowledge the contradiction
• Example: “While preliminary findings suggested X (Author, 2024, preprint), subsequent peer-reviewed research demonstrated Y (Author, 2025, Journal). Our study builds on the revised understanding…”
• Shows you’re current with evolving knowledge

If discovered during revision:

• Address directly in response to reviewers
• Revise relevant text sections
• Example: “Thank you for noting that recent publications have contradicted the preprint we cited. We have revised our interpretation in Section [X] to reflect the current evidence base.”

Graceful acknowledgment in discussion:

"Our initial hypothesis was informed by preliminary findings (Author et al., 2024, preprint) that suggested X. However, peer-reviewed analysis (Author et al., 2025; Other et al., 2025) has since revealed Y. While our experimental design was based on the preprint model, our findings actually align better with the revised understanding, suggesting..."

This approach:

• Demonstrates scientific integrity
• Shows awareness of evolving evidence
• Turns a potential weakness into a strength
• Reviewers appreciate honesty about changing landscapes

Prevention Strategies: Evaluating Preprint Quality Before Citing

Risk assessment framework:

Lower-risk preprints (safer to cite):

• ✅ Authors with strong publication records in this area
• ✅ Reputable institutions
• ✅ Methods thoroughly described and standard
• ✅ Claims proportionate to evidence
• ✅ Multiple versions showing refinement (suggests author responsiveness)
• ✅ Positive comments/endorsements on preprint server
• ✅ Already accepted for publication (journal noted)

Higher-risk preprints (use caution):

• ⚠️ First-time authors with no publication record
• ⚠️ Unknown or questionable institutional affiliations
• ⚠️ Methods poorly described or non-standard
• ⚠️ Extraordinary claims without extraordinary evidence
• ⚠️ Only version 1 with no updates despite being months old
• ⚠️ Critical comments or concerns in preprint discussions
• ⚠️ Contradicts well-established findings without strong rationale

Red flags suggesting potential problems:

• 🚩 Claims that seem too good to be true
• 🚩 Methods that skip standard controls
• 🚩 Statistical analyses that seem questionable
• 🚩 Figures that appear manipulated or poorly presented
• 🚩 References that don’t support claims made
• 🚩 Authors anonymous or using pseudonyms
• 🚩 Posted to multiple servers (might indicate rejection from others)

Quality checks before citing:

1. Read yourself critically – Would this pass peer review as is?
2. Check author track records – Do they have credible publication histories?
3. Examine methodology – Are methods sound and well-described?
4. Proportionality test – Are claims proportionate to

evidence? 5. Community reception – What do comments and early citations suggest? 6. Cross-reference – Does this align with or contradict established knowledge?

Post-Publication Peer Review Resources

Where to check for preprint criticism:

PubPeer (https://pubpeer.com/)

• Post-publication peer review platform
• Scientists comment on preprints and publications
• Search by DOI or title
• Anonymous or attributed comments

PreReview (https://prereview.org/)

• Community-driven preprint review
• More structured than comments
• Growing but not comprehensive

Preprint server comments

• bioRxiv, medRxiv allow commenting
• arXiv has trackbacks showing citations
• Not all preprints receive comments

Twitter/X science community

• Scientists often discuss preprints
• Search for preprint DOI or title
• Can reveal concerns or enthusiasm
• Take with a grain of salt (not always expert opinion)

Journal clubs and blogs

• Some labs discuss preprints in journal clubs
• Science blogs sometimes review preprints
• Look for thoughtful analysis, not just hot takes

Your own professional network

• Ask colleagues in the specific subfield
• Conference discussions often reveal preprint reception
• Informal peer review through community knowledge

Understanding the journal editorial decision process can help you anticipate how reviewers might evaluate manuscripts citing retracted or controversial preprints.

Common Mistakes When Citing Preprints (And How to Avoid Them)

Even experienced researchers make preventable errors when citing preprints. These mistakes can trigger reviewer concerns or weaken your manuscript unnecessarily.

Mistake #1: Not Indicating Preprint Status

The problem:

• Preprint cited exactly like a published article
• No “[Preprint]” notation in reference
• No mention of preprint status in text
• Readers assume it’s peer-reviewed

Why this is bad:

• Misleads readers about evidence quality
• Reviewers may assume you don’t know it’s a preprint
• Violates transparency principles
• May violate journal citation policies

Example of what NOT to do:

Smith, J., & Jones, M. (2025). Important findings in neuroscience. bioRxiv.

Without “[Preprint]” notation, this looks like a journal named “bioRxiv.”

How to fix it:

APA format (correct):

Smith, J., & Jones, M. (2025). Important findings in neuroscience. bioRxiv. https://doi.org/10.1101/2025.01.15.123456

(Repository name makes preprint status clear)

NLM format (correct):

Smith J, Jones M. Important findings in neuroscience. bioRxiv [Preprint]. 2025 Jan 15. Available from: https://doi.org/10.1101/2025.01.15.123456

(Explicit “[Preprint]” notation)

In-text mention (good practice):

• First citation: “Recent preliminary findings (Smith & Jones, 2025, preprint) suggest…”
• Subsequent citations: “(Smith & Jones, 2025)” [status established]

Mistake #2: Missing or Incorrect Version Numbers

The problem:

• Preprints are frequently updated
• Different versions may have different findings
• Citing without a version specification is ambiguous
• You might cite v1, but readers find v3 with different conclusions

Why versioning matters:

Example scenario:

• v1 (Jan 2025): Claims Effect X is significant (p=0.03)
• v2 (Feb 2025): Corrects statistical error, Effect X not significant (p=0.18)
• v3 (Mar 2025): Adds new data, Effect X significant again with better power (p=0.001)

If you cite “Smith et al., 2025” without a version, which findings are you referencing?

How to cite versions correctly:

When version is important (findings changed):

Smith, J., & Jones, M. (2025). Important findings, version 2. bioRxiv. https://doi.org/10.1101/2025.01.15.123456v2

When discussing evolution across versions:

"Initial findings (Smith & Jones, 2025, bioRxiv v1) suggested X; however, after methodological revision, updated analyses (Smith & Jones, 2025, bioRxiv v3) demonstrated Y."

Best practice:

• Always check the current version before finalizing the manuscript
• Cite the version you actually read and relied on
• Note if discussing a specific version versus the most current
• Update to the latest version during revision if appropriate

Mistake #3: No DOI or Using Unstable URLs

The problem:

• Citing preprints with direct URLs instead of DOIs
• URLs may change or break
• Readers can’t find the preprint
• Violates citation permanence principles

Bad examples:

❌ Smith, J. (2025). Findings. Retrieved from https://www.biorxiv.org/content/10.1101/2025.01.15.123456v1.full.pdf

❌ Jones, M. (2025). Research. Available at: biorxiv.org/content/early/2025/01/15/2025.01.15.123456

❌ Brown, K. (2025). Study. See: biorxiv.org/cgi/content/short/2025.01.15.123456v1

Problems with these:

• URLs may redirect or change
• PDF links may break
• “Early” versions get moved
• Not following DOI standards

Correct approach (use DOI):

✅ Smith, J. (2025). Findings. bioRxiv. https://doi.org/10.1101/2025.01.15.123456

Why DOIs are better:

• Permanent identifiers
• Resolve even if the repository changes
• Standard academic citation practice
• Enable CrossRef tracking
• Work with citation management software

Finding DOIs:

• All major preprint servers assign DOIs
• Look at the preprint page header
• Usually formatted: 10.1101/YYYY.MM.DD.######
• If no DOI exists, question the repository legitimacy

Mistake #4: Treating Preprints Like Published Articles in Text

The problem:

• Language suggests peer-reviewed validation
• Claims presented without hedging
• Failing to acknowledge the preliminary status

Problematic examples:

❌ Too confident:

"Smith et al. (2025) demonstrated that Treatment X cures Disease Y."

(A preprint hasn’t “demonstrated” anything definitively)

❌ Uncritical acceptance:

"Research proves that X causes Y (Jones et al., 2025)."

(Preprints don’t “prove” – they present preliminary findings)

❌ Inappropriate authority:

"According to established findings (Author et al., 2025)..."

(Preprints aren’t “established”)

Better approaches:

✅ Appropriately hedged:

"Preliminary findings suggest that Treatment X may be effective for Disease Y (Smith et al., 2025, preprint)."

✅ Acknowledges status:

"Recent unreviewed work by Jones and colleagues (2025, bioRxiv preprint) reported a correlation between X and Y."

✅ Contextualizes uncertainty:

"While awaiting peer review, initial data (Author et al., 2025, preprint) indicate..."

Hedging language for preprints:

• “Preliminary findings suggest…”
• “Initial results indicate…”
• “Preprint data show…”
• “Unreviewed work reports…”
• “Early evidence suggests…”
• “According to preprint findings…”

This doesn’t mean being dismissive:

• Don’t say “merely a preprint” or “just preliminary”
• Balance acknowledgment of status with respect for the work
• The goal is transparency, not denigration

Mistake #5: Citing Superseded or Outdated Versions

The problem:

• Citing an old version when a newer version exists
• Methodology or conclusions changed in updates
• You’re discussing findings that the authors have revised

How this happens:

• You downloaded v1 months ago
• Authors posted v2 and v3 since then
• You didn’t check for updates before submission
• Your citation refers to outdated information

Real-world example:

You cite: "Smith et al. (2025) found no effect of X on Y."

Current version actually says: "After correcting the analysis error noted in v1, we now find a significant effect of X on Y (p<0.001)."

Reviewer reads current version and thinks: "This author is citing findings that have been corrected. Did they even read the paper?"

How to avoid:

• Check the preprint page immediately before finalizing the manuscript
• Look for “Revisions” or “Version history.”
• Read update notes if provided
• During revision, check again (months may have passed)
• Set alerts for preprints you’re monitoring

When to cite old versions:

• You’re specifically discussing how findings evolved
• You’re analyzing the preprint revision process itself
• You need to reference the original hypothesis before revision

Format for discussing evolution:

"Initial analyses (Smith et al., 2025, bioRxiv v1) found no effect; however, after methodological refinement (Smith et al., 2025, bioRxiv v3), significant effects emerged."

Mistake #6: Over-Reliance on Preprints When Peer-Reviewed Alternatives Exist

The problem:

• Multiple preprints cited when peer-reviewed papers cover the same ground
• Appears like a lazy literature review
• Suggests you’re not reading established literature
• Weakens evidence base unnecessarily

Example of over-reliance:

Reference list shows:
- 15 bioRxiv preprints
- 5 peer-reviewed articles

Reviewer thinks: “Why is this author citing so many preprints? Are they not reading the published literature? Are they trying to make the reference list look longer?”

When this is appropriate:

• Very new field where preprints dominate
• Physics/math where arXiv is standard
• Discussing cutting-edge work from the last 3-6 months

When this is problematic:

• Established fields with robust peer-reviewed literature
• Medical/clinical research where peer review is valued
• When similar peer-reviewed sources exist but weren’t cited

Balance check:

• Review your reference list
• Are preprints >20-30% of total citations? (Except in physics/math/CS)
• For each preprint, ask: “Is there a peer-reviewed alternative?”
• Prioritize peer-reviewed when quality is equivalent

Showing literature depth:

• Mix of historical foundational papers
• Recent peer-reviewed work
• Select cutting-edge preprints where appropriate
• Demonstrates a comprehensive, balanced review

Mistake #7: Inconsistent Citation Formatting

The problem:

• Some preprints cited with “[Preprint]” notation
• Others without a clear indication
• Mixing formats within the same manuscript
• Appears careless or confusing

Example of inconsistency:

Reference 12: Smith, J. (2025). Study A. bioRxiv. https://doi.org/...
Reference 15: Jones, M. (2025). Study B [Preprint]. bioRxiv. https://doi.org/...
Reference 23: Brown, K. (2025). Study C. Available at bioRxiv.org...

Why this is bad:

• Confuses readers about status
• Suggests lack of attention to detail
• Makes your manuscript look less professional
• Reviewers notice formatting inconsistencies

How to fix:

• Choose one format for all preprints (follow your style guide)
• Use Find/Replace to ensure consistency
• Create a citation style template
• Have the co-author specifically check the preprint citation formatting

Consistency checklist:

• All preprints use the same notation style
• All include the repository name
• All include DOIs when available
• All follow the same version notation (if applicable)
• In-text citations consistently mention “preprint” or not

Mistake #8: Citing Preprints Without Actually Reading Them

The problem (yes, this happens):

• Citing based on the abstract alone
• Finding a preprint in someone else’s reference list and citing without reading
• Assuming the preprint says what the title suggests

Why this is especially risky with preprints:

• No peer review to catch errors before you cite them
• Methodology might be flawed
• Claims might be overstated
• Conclusions might not match your interpretation

Reviewer red flags:

• You cite the preprint, but your interpretation doesn’t match its findings
• You cite contradictory preprints without acknowledging the contradiction
• You attribute claims to preprints that don’t make those claims

Best practice:

• Read every preprint you cite (at minimum: intro, methods, results, discussion)
• Verify the claims you’re attributing
• Check if your interpretation matches the authors’ conclusions
• Assess methodology quality yourself

Especially important for preprints because:

• Peer reviewers haven’t evaluated quality
• You’re responsible for critical evaluation
• Errors in the preprints you cite reflect on your judgment

The Future of Preprint Citations in Academic Publishing

Understanding emerging trends helps you anticipate how preprint citation practices will evolve and position your work accordingly.

Increasing Acceptance and Normalization

Current trajectory:

The trend toward preprint acceptance shows no signs of reversing. By 2030, predictions suggest:

• 80-90% of journals will explicitly allow preprint citations (up from ~70% in 2026)
• Preprint posting will be standard practice in most STEM fields
• Social sciences will approach natural science levels of preprint adoption
• Even conservative medical journals will soften policies (except perhaps NEJM)

Driving factors:

• Generational change (younger researchers grew up with preprints)
• Funder mandates increasingly recognize preprints
• Open science movements gaining institutional support
• COVID-19 permanently shifted cultural norms
• Competition for rapid communication

What this means for you:

• Citing preprints will become less controversial over time
• Current conservative journals may relax policies
• Skills in evaluating preprint quality will be increasingly valuable
• Understanding preprint ecosystems will be essential research literacy

Better Integration and Infrastructure

Technical improvements underway:

Version tracking:

• Automated systems linking preprint versions to publications
• CrossRef improvements enabling better version discovery
• DOI families connecting related versions
• Citation software automatically detecting updates

Quality indicators emerging:

• Preprint review services (eLife, Review Commons, PREreview)
• Community ratings and endorsements
• AI-based quality screening tools (SciScore, Statcheck integration)
• Transparent metrics (downloads, citations, discussion activity)

Discovery and search:

• Google Scholar improving preprint indexing
• PubMed expanding preprint coverage
• Discipline-specific search tools incorporating preprints
• Alert systems for preprint-to-publication transitions

Publisher integration:

• Journal submission systems accepting preprint transfers
• Streamlined workflows from preprint to peer review
• Portable peer review (reviews following preprints across journals)
• Co-publication models (preprint + journal simultaneously)

What this means for researchers:

• Finding published versions will become easier
• Tracking preprint evolution will be more seamless
• Quality assessment will have better tools
• Citation management will be less manual

Preprint Citation Index and Metrics

Web of Science Preprint Citation Index (launched 2022):

Currently indexes preprints from:

• arXiv
• bioRxiv
• ChemRxiv
• medRxiv
• Research Square
• SSRN (selective)

Implications:

• Preprints now generate formal citation metrics
• Contributes to author H-index and impact
• Legitimizes preprints as scholarly outputs
• Universities increasingly count preprints in evaluations

Future developments:

• More repositories will be indexed
• Altmetrics for preprints will mature
• Differentiation between preprint and publication citations
• Tracking preprint influence separate from publication impact

What this changes:

• Preprint citations “count” for academic credit
• Incentivizes preprint posting
• Makes preprint citation more acceptable
• Provides data for studying preprint ecosystems

Post-Publication and Pre-Publication Peer Review Integration

Emerging models:

Overlay journals:

• Curate and provide peer review for existing preprints
• Don’t host content, just add validation layer
• Examples: Discrete Analysis (math), biOverlay (proposed)

Preprint review platforms:

• PREreview: Structured community review of preprints
• Review Commons: Portable peer review across journals
• eLife: Public peer review of preprints before traditional publication

Hybrid models:

• Preprint posted → Community review → Journal publication
• Continuous improvement through open feedback
• Transparent peer review visible on preprint page

Publisher experimentation:

• eLife model: Post preprints, conduct peer review publicly, publish reviews alongside
• PLoS ONE: Considering integrating preprints more deeply
• Frontiers: Exploring post-publication curation of preprints

What this means for citing preprints:

• Some preprints will have semi-formal review status
• “Reviewed preprint” may become a citable category
• Quality signals will be more nuanced than preprint/published binary
• Citation practices may need to distinguish reviewed vs. non-reviewed preprints

Challenges and Concerns on the Horizon

Not everyone is enthusiastic about preprint expansion:

Quality control concerns:

• Flood of low-quality preprints diluting signal
• Predatory preprint servers emerging (already happening)
• Public confusion about peer review status
• Media misreporting preliminary findings as established

Misinformation risks:

• COVID-19 showed how preprints can spread misinformation
• Ivermectin, hydroxychloroquine controversies involved preprints
• Public health implications of incorrect preliminary findings
• Balance between rapid communication and accuracy

Intellectual property issues:

• Patent considerations with public preprint posting
• Industry researchers hesitant to post preprints
• Competitive concerns in commercial research
• Scooping anxiety (though mostly unfounded)

Publication system disruption:

• If preprints become primary mode, what’s journals’ role?
• Business model implications for publishers
• Quality control mechanisms if peer review diminishes
• Career evaluation if preprints replace publications

Field-specific resistance:

• Humanities still skeptical of preprint value
• Clinical medicine maintaining caution
• Some societies protecting traditional journal revenue
• Generational divides in acceptance

Predictions for 2030

Very likely:

• Preprint citation will be universal in STEM fields
• Most journals will have explicit, supportive preprint policies
• Citation management software will seamlessly handle preprint-publication linking
• Preprint metrics will be standard in research evaluation

Probable:

• Social sciences will have preprint cultures similar to current biology
• Some form of quality badging/review will be standard on preprints
• Journals will increasingly integrate with preprint servers
• Medical journals will accept preprint citations with less controversy

Possible:

• Humanities develops robust preprint culture
• Traditional peer review significantly changes due to preprint models
• Preprints partially replace journals in some fields
• New publication models emerge blurring preprint/publication distinction

What remains uncertain:

• Whether quality control mechanisms will keep pace with preprint growth
• How the public will understand preprint vs. publication distinctions
• Whether predatory preprint servers will become a major problem
• How intellectual property law will adapt

Preparing for this future:

• Develop critical evaluation skills for preprints
• Stay current with evolving policies in your field
• Learn to use preprint infrastructure effectively
• Understand both benefits and limitations of preprint systems
• Contribute to responsible preprint culture development

Understanding these trajectories helps you make informed decisions about citing preprints today while anticipating how practices will evolve throughout your career.

Frequently Asked Questions

Q: Can I cite a preprint if there’s no peer-reviewed version available?

Yes, absolutely. This is one of the primary legitimate uses of preprint citations—when the work hasn’t yet been published in a peer-reviewed journal but represents important recent developments in your field. Just ensure you clearly indicate the preprint status in your citation and mention it in the text where appropriate (e.g., “recent preliminary findings,” “according to preprint data”). Always check your target journal’s policy to confirm they allow preprint citations.

Q: What if the preprint I cited gets retracted after my paper is published?

If a preprint you cited is retracted after your paper is published, the appropriate response depends on how central that citation was to your work. For minor contextual citations, typically no action is needed—the scientific record naturally evolves. For citations central to your argument or conclusions, contact your journal’s editors about potentially issuing a correction or addendum. Most journals have processes for addressing this situation. The key is transparency—if someone asks, be upfront about the retraction and how it affects (or doesn’t affect) your findings.

Q: Do preprint citations “count” for my H-index and citation metrics?

Yes, increasingly they do. The Web of Science Preprint Citation Index (launched 2022) now indexes citations to and from preprints for major repositories including arXiv, bioRxiv, and others. Google Scholar has indexed preprints for years. However, some university evaluation systems and funding agencies still don’t fully count preprints the same as peer-reviewed publications. This is changing rapidly—many institutions now explicitly recognize preprints in promotion and tenure decisions, especially post-COVID-19. Check your specific institution’s policies.

Q: Should I cite the preprint or the published version if both exist?

Always cite the published, peer-reviewed version unless you have a specific reason to reference the preprint. The published version is more authoritative, has undergone peer review, and is the permanent scholarly record. The only exceptions are when you’re specifically discussing how findings evolved from preprint to publication, or when the preprint version contains information not in the published version. Citing a preprint when the published version exists makes your literature review appear outdated or careless.

Q: How do I know if a preprint has been published in a journal?

Check multiple sources: (1) Visit the preprint server page—many now display “Published in [Journal]” banners at the top; (2) Google Scholar search for the authors and title; (3) PubMed search if it’s biomedical research; (4) Check the authors’ institutional or personal websites; (5) Look for CrossRef links on the preprint DOI page. Set up Google Scholar alerts for important preprints you’re monitoring so you’ll be notified when they’re formally published. Always do a final check immediately before submitting your manuscript.

Q: Are there fields where citing preprints is inappropriate or discouraged?

Yes, field norms vary significantly. Medicine and clinical research remain more conservative, with some journals (notably NEJM) maintaining restrictions. Humanities fields have minimal preprint culture and citations are rare. Some traditional society journals across disciplines still discourage preprints. Always check your specific target journal’s author guidelines. That said, the trend across almost all fields is toward increasing acceptance. Even in cautious fields, preprint citations are becoming more common, especially for methodological references or very recent developments where no peer-reviewed alternative exists.

Q: What’s the difference between citing a preprint from arXiv vs. bioRxiv vs. other servers?

The main difference is field-specific norms and historical acceptance. arXiv (physics, math, CS) has 30+ years of acceptance and is considered completely standard—many landmark papers exist only on arXiv. bioRxiv (biology) is newer (2013) but now widely accepted post-COVID. medRxiv (medicine) is newer still (2019) and faces more scrutiny. The repository matters less than: (1) whether it’s a legitimate, reputable server (the ones mentioned are), (2) whether your field uses it, and (3) whether your target journal accepts preprint citations generally. Cite from the repository where the authors posted it, and follow your style guide for formatting.

Q: Can I cite my own preprint in my journal submission?

Yes, you can cite your own preprints in journal submissions. This is common when you have related work that’s posted but not yet published, or when you want to reference methods detailed in a preprint. However, some journals have specific policies about self-citation of preprints versus published work. If you’re submitting manuscript A to a journal and it cites your own preprint B, that’s typically fine. What’s generally not acceptable is posting manuscript A as a preprint and then submitting it to a journal that prohibits prior public posting (like NEJM’s Ingelfinger Rule). Always check specific journal policies.

Q: How recent does a preprint need to be for it to be acceptable to cite?

There’s no hard rule, but context matters. Very old preprints (5+ years) that were never formally published may raise questions—why wasn’t it published? Was it rejected? Are the findings flawed? In physics and mathematics, old arXiv papers are completely normal as some important work remains only on arXiv. In biology and medicine, a 3-5 year old bioRxiv preprint that was never published is more suspicious. Always ask: Why hasn’t this been peer-reviewed and published? If there’s a good reason (niche topic, author moved to industry, chosen to remain preprint), it’s fine. If the reason is unclear, evaluate quality extra carefully or find alternatives.

Q: What if reviewers object to my preprint citations?

If reviewers object to your preprint citations, respond professionally and be willing to compromise. First, determine if they have a substantive concern (“this preprint has been contradicted”) versus a philosophical objection (“preprints shouldn’t be cited”). For substantive concerns, update or replace citations as needed. For philosophical objections, you have options: (1) If the journal allows preprints, politely note this in your response and explain why the citation is necessary; (2) If alternative peer-reviewed sources exist, replace them to avoid conflict; (3) If the preprint is genuinely essential and irreplaceable, make your case clearly. Understanding how to respond to reviewer comments diplomatically while maintaining scientific integrity is key.

Q: Do I need to indicate preprint status every time I cite the same preprint in my text?

No, you don’t need to say “preprint” every single time. Best practice: Indicate preprint status at first mention in your text (e.g., “Recent preliminary findings (Smith et al., 2025, preprint) suggest…”), and ensure your reference list clearly shows it’s a preprint. After establishing status, you can cite normally throughout your manuscript (Smith et al., 2025). Readers will remember from the first mention and can check the reference list. Repeatedly saying “preprint” can become awkward and interrupt flow. The key is transparency at first mention and clear notation in references.

Conclusion: Citing Preprints Strategically and Responsibly

Preprint citations have evolved from controversial practice to mainstream scholarly communication in less than a decade. While acceptance varies by field and journal, the trajectory is clear: preprints are becoming permanent features of academic publishing, and citing them appropriately is an essential research skill.

Key principles for responsible preprint citation:

Transparency: Always clearly indicate preprint status in both reference lists and in-text mentions. Readers and reviewers should never be left uncertain about whether a source has been peer-reviewed.

Quality evaluation: Exercise critical judgment when citing preprints. Without peer review as a quality filter, you bear more responsibility for evaluating methodology, assessing claims, and determining credibility.

Field awareness: Understand your discipline’s specific norms. What’s standard in physics may be controversial in medicine. Adapt your citation practices to align with both field expectations and target journal policies.

Strategic timing: Check whether preprints you’ve cited have been published before finalizing your manuscript. Always prioritize peer-reviewed versions when available.

Appropriate hedging: Frame preprint-based claims with appropriate tentativeness. Use language like “preliminary findings suggest” rather than “research proves.”

Balanced use: Don’t over-rely on preprints when peer-reviewed alternatives exist. Mix cutting-edge preprint citations with established literature to demonstrate comprehensive scholarship.

When Preprint Citations Strengthen Your Work

Preprint citations demonstrate:

• Engagement with current research conversations
• Awareness of recent developments
• Commitment to comprehensive literature coverage
• Understanding of evolving knowledge

They’re especially valuable when:

• Discussing genuinely cutting-edge science
• Working in fields with established preprint cultures
• Providing methodological context from recent work
• Demonstrating thorough literature searches

When to Exercise Caution

Consider alternatives to preprint citations when:

• Peer-reviewed sources cover the same ground
• Your target journal discourages preprints
• Medical or clinical claims require validation
• The preprint quality is uncertain
• Core arguments depend entirely on unreviewed work

Looking Forward

As preprint infrastructure matures and academic culture continues evolving, citing preprints will become increasingly routine across disciplines. The researchers who succeed will be those who can:

• Evaluate preprint quality critically
• Navigate field-specific norms strategically
• Balance innovation with appropriate caution
• Contribute to responsible preprint ecosystems

Understanding how to choose the right journal for your work, including considering their preprint policies, is part of strategic manuscript preparation. Similarly, knowing how to handle various types of journal decisions prepares you for the full publication process.

Preprints represent both opportunity and responsibility. Used strategically and cited responsibly, they enhance your scholarship and contribute to faster, more open scientific communication. The key is balancing enthusiasm for rapid knowledge sharing with commitment to quality, transparency, and intellectual integrity.

Your ability to navigate this evolving landscape—citing preprints when appropriate, evaluating their quality critically, and following field-specific norms—marks you as a sophisticated participant in contemporary academic discourse.

About the Author

Dr. James Richardson is a research engineer with extensive experience navigating academic publishing across multiple disciplines. Throughout his career, he has both authored numerous preprints and served as a peer reviewer evaluating manuscripts that cite them. This dual perspective—as both preprint author and consumer—informs his practical guidance on when and how to cite preprints effectively.

Dr. Richardson’s expertise spans the evolution of preprint culture from the early days of arXiv through the rapid expansion during COVID-19. He has published research in journals with varying preprint policies, from traditional societies maintaining conservative stances to progressive open-access publishers leading preprint integration. His work has appeared in venues indexed by Web of Science, PubMed, and major discipline-specific databases.

As a reviewer, Dr. Richardson has evaluated hundreds of manuscripts containing preprint citations, observing common pitfalls and effective strategies firsthand. He brings this practical editorial perspective to his writing, helping researchers navigate the complexities of citing preliminary work while maintaining scholarly rigor.

This guide reflects his commitment to helping researchers—especially early-career scholars and PhD students—understand rapidly evolving publication norms. Dr. Richardson believes that preprints, when used responsibly, strengthen scientific communication by accelerating knowledge sharing while maintaining quality through thoughtful evaluation.

His insights draw from direct experience with preprint servers including arXiv, bioRxiv, medRxiv, and SSRN, as well as engagement with emerging preprint review platforms and overlay journals. He remains actively involved in discussions about the future of scholarly communication and the role of preprints in open science.

Questions about preprint citation practices? The comment section below includes discussions of specific scenarios and field-specific guidance. Share your experiences to help other researchers navigate this evolving landscape.

Last Updated: January 2026 | Next Review: April 2026

This guide is updated quarterly to reflect evolving journal policies, new preprint infrastructure, and emerging best practices. Bookmark this page for future reference when preparing your manuscript submissions.