How to Respond to Peer Reviewer Comments
Getting a "major revision" decision doesn't mean the paper failed. It means it passed the first hurdle. Most papers accepted at top journals go through at least one major revision. The revision stage is where manuscripts are won or lost.
How you respond to reviewers matters as much as what experiments you run. Editors read the response letter closely. It's evidence of how seriously you took the critique and whether you understood it. This guide covers format, tone, and specific tactics for common revision scenarios.
The Right Mindset Going In
Reviewers are almost always trying to help
Even harsh reviews usually point to real weaknesses. A reviewer who says your controls are insufficient may be saving you from a future retraction. Read negative reviews twice before reacting.
You don't have to do everything
You can disagree with reviewer requests, but you have to explain why, respectfully and with evidence. Refusing a request without explanation reads as dismissive. Refusing with a clear scientific rationale is legitimate.
The editor is your audience, not the reviewer
The response letter goes to the editor, who then decides whether your revisions adequately address the reviewers. Write for the editor who may be less expert than the reviewer. Clarity wins over technical density.
Format: The Point-by-Point Response
Every top journal expects a point-by-point response letter. The format is standard: quote each reviewer comment, then respond immediately below. Here's what a well-structured response looks like:
Structure template
Dear Editors and Reviewers,
We thank the reviewers for their careful reading and constructive comments. We have addressed all concerns as described below. Changes to the manuscript are highlighted in yellow in the revised version.
REVIEWER 1
Comment 1.1: "The authors should include additional controls for [X] to rule out [alternative explanation]."
Response:
We thank the reviewer for this suggestion. We have added [specific experiment] in Figure [X], which demonstrates [result]. This rules out [alternative explanation] because [reason]. The manuscript has been revised to include this data on page [X], lines [X–X].
Handling Specific Scenarios
Scenario: You disagree with a reviewer request
Acknowledge the concern behind the request, explain why the experiment isn't feasible or why it wouldn't resolve the concern as the reviewer expects, and offer an alternative. Frame it as a scientific argument, not a refusal. 'While we understand Reviewer 2's concern about X, we believe this experiment would not resolve the issue because [reason]. Instead, we have addressed this by [alternative].'
Scenario: Two reviewers contradict each other
Address both directly and explicitly flag the contradiction. 'Reviewer 1 requested X, while Reviewer 2 suggested the opposite approach Y. We have followed Reviewer 1's suggestion because [rationale], and we believe this approach better addresses the underlying concern about [issue].' Let the editor resolve the disagreement. Your job is to be transparent about it.
Scenario: A reviewer requests experiments you can't do (time, cost, ethics)
Explain why the experiment isn't feasible: be specific, not vague. 'This experiment would require access to a patient cohort we don't have. We have instead cited [published reference] which supports this conclusion in a larger sample.' Or for timeline constraints: acknowledge the limitation explicitly in the manuscript rather than pretending it doesn't exist.
Scenario: A reviewer seems to have misunderstood your work
Don't say 'the reviewer misunderstood.' Say 'we may not have been sufficiently clear about X.' Then clarify in the response AND in the revised manuscript. Even if the reviewer was wrong, the fact that they misunderstood means your writing wasn't clear enough. Fix both.
Scenario: You've been asked to shorten the manuscript significantly
Take this seriously: editors make these requests because reviewers found the paper overlong, not as an arbitrary constraint. Cut ruthlessly. State in the response what you removed and why, and confirm the new word count. Submitting an only marginally shortened manuscript after being asked to cut by 20% signals that you didn't take the request seriously.
Tone: What Editors Notice
Tone that works
- • Professional and collegial, since they're peers, not adversaries
- • Specific. Reference exact data, exact pages, exact figures
- • Appreciative without being sycophantic. One genuine thanks is enough
- • Confident when you disagree: assert your scientific rationale clearly
Tone to avoid
- • Defensive or combative: even when a reviewer is wrong, anger reads badly to the editor
- • Dismissive ("as we clearly stated in the original..."): this antagonizes reviewers
- • Over-grateful ("we are deeply thankful for every insightful comment..."): reads as hollow
- • Passive-aggressive ("we have made this change, although we believe it weakens the paper"): if you believe the change hurts the paper, say so directly and argue against it
Revision Timeline
Most journals give you 1–3 months for a major revision and 2–4 weeks for a minor revision. If you need more time, ask: journals almost always grant extensions if you communicate early and specifically ("we need 4 months because of [new experiment required]", not just "we need more time").
Don't take longer than you need to be thorough. A revision returned in 6 weeks is not inherently better than one returned in 3 months: what matters is whether every concern was genuinely addressed. But journals notice when revisions are returned very quickly without substantial new data, which can raise questions about whether the experiments were actually run.
References
- Committee on Publication Ethics (COPE). (2017). Ethical Guidelines for Peer Reviewers. Retrieved February 2026. [publicationethics.org ↗]
- Annesley TM. Responding to reviewer comments. Clin Chem. 2011;57(4):551-554. [doi.org/10.1373/clinchem.2011.162388 ↗]
- Nature Portfolio. How to write a rebuttal letter. Springer Nature Author and Reviewer Services. Retrieved February 2026. [masterclasses.nature.com ↗]
- Noble WS. Ten simple rules for responding to reviewer comments. PLoS Comput Biol. 2017;13(10):e1005730. [doi.org/10.1371/journal.pcbi.1005730 ↗]
- International Committee of Medical Journal Editors (ICMJE). Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals. Retrieved February 2026. [icmje.org ↗]
Suggested Citation
APA
Manusights. (2026). How to respond to peer reviewer comments: A guide for biomedical authors. Retrieved from https://manusights.com/resources/responding-to-reviewers
MLA
Manusights. "How to Respond to Peer Reviewer Comments: A Guide for Biomedical Authors." Manusights, 2026, manusights.com/resources/responding-to-reviewers.
VANCOUVER
Manusights. How to respond to peer reviewer comments: a guide for biomedical authors [Internet]. 2026. Available from: https://manusights.com/resources/responding-to-reviewers
CC BY 4.0 - share and adapt freely with attribution to Manusights (manusights.com/resources).
Frequently Asked Questions
How long do I have to respond to reviewer comments?
Most journals give authors 30 to 90 days to submit a revised manuscript after a major revision decision. Nature family journals typically allow 3 months. Cell Press journals allow 2 months with one extension possible. NEJM and JAMA allow 60-90 days. Some journals let you request an extension - it's almost always granted for major revisions. Track the deadline in the decision email, and if you need more time, contact the editorial office before the deadline expires. Late submissions without communication often trigger automatic withdrawal.
Do I have to do everything the reviewers ask?
No - but you must address every comment, even the ones you disagree with. For requests you won't fulfill, write a polite, evidence-based rebuttal explaining why the requested change would not improve the paper or is outside the scope of the study. Editors expect authors to push back professionally on unreasonable requests. What editors don't accept is ignoring a comment entirely. Every reviewer point needs a response in your cover letter, even if that response is a well-argued "we respectfully disagree because..." followed by supporting citations or data.
What format should my response to reviewers take?
The standard format is a point-by-point response letter. Start with a brief thank-you to the editor and reviewers. Then address each reviewer separately (Reviewer 1, Reviewer 2, etc.), quoting each comment verbatim and providing your response directly below it. For each change made to the manuscript, include the exact revised text with line numbers or page references. Use clear visual separation between reviewer comments and your responses. A clean, organized response letter signals competence and makes the editor's job much easier.
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