How to respond to peer reviewer comments: a structured approach

A major or minor revision is not a rejection in disguise. It means the editor saw a publishable paper inside your manuscript and is giving you a formal chance to produce it. What decides the outcome is usually not the brilliance of the study but the clarity of the response letter, because the editor reads your responses before re-reading the paper.

What the editor is actually asking for

Strip away the individual comments and a revision request asks three questions. Did you understand every point raised? Did the manuscript genuinely change where it needed to? And where you did not change it, is that a defensible scientific decision rather than stubbornness? A good response letter answers all three in its opening paragraph and then proves them point by point.

Before you write a single response

• Read the decision letter once, then leave it for a day. First reactions to criticism are rarely your most useful ones.
• Build a numbered master list of every comment, including brief editorial remarks. Reviewers notice within seconds if a number has no answer.
• Merge comments that point at the same underlying problem and answer them together, cross-referencing the numbers.
• Decide early what you will not change. Knowing your red lines before you start writing prevents reluctant, half-applied revisions.
• Check the deadline honestly. If clinical duties or data work make it unrealistic, request an extension before it expires; editors grant reasonable ones routinely.

The response-letter structure editors prefer

Open with a short summary: the main changes, the sections most affected, and anything you declined to do with a one-line reason. Then answer every comment in order, quoting the comment before each answer so nobody has to cross-reference two documents. Where a change is identical across the manuscript — terminology, a relabelled figure, a corrected abbreviation — say so once and list the pages affected.

Keep the letter findable: the reviewer who wrote comment 14 should locate your answer to comment 14 in under ten seconds. Editors forgive plain formatting; they do not forgive hunting.

How to answer an individual comment

A workable pattern for each point is: acknowledge the comment in one clause, answer the substance, show the change, and give its location. Quoting the revised sentence from the manuscript is stronger than describing what you changed, because the reviewer can verify it without opening a tracked-changes file.

Two cases need extra care. Statistical queries deserve a real answer, not reassurance: if a reviewer questions a test, an assumption or a sample-size justification, have the analysis rechecked and respond with the method and the numbers. And new results must live in the manuscript or supplementary files with methods attached — a result that exists only in the response letter does not exist at all.

When to disagree with a reviewer

Disagreement is allowed, and often correct: reviewers are advisors, not co-authors, and the authors remain responsible for the science. Disagree with evidence rather than tone. Cite the reporting guideline, the published method or the standard you followed, and explain why it fits this study. If two reviewers contradict each other, say so plainly and ask the editor to arbitrate; that is what editors are for. What never works is silent refusal — skipping a comment — or agreeing in the letter while leaving the manuscript unchanged.

Six mistakes that turn a revision into a rejection

• Answering most comments instead of all of them. One skipped point can sink an otherwise excellent response.
• Debating a reviewer's tone instead of their argument. Editors remember tone long after they forget the dispute.
• Hiding changes. If a paragraph moved, a figure was replaced or the author list changed, say so explicitly.
• New analyses without methods, or conclusions that drift beyond the new data.
• Missing the deadline without asking for an extension first.
• Treating a statistical critique as a matter of opinion. Get it checked before you respond, not after.

Sources and further reading

• COPE Core Practices — responsible peer review and author responsibilities during revision.
• ICMJE Recommendations — revisions, communication with editors and changes to authorship.
• EQUATOR Network — re-check your report against the study-specific checklist before resubmission.
• How to verify journal indexing — before you resubmit anywhere, confirm the journal is genuinely indexed.
• How to identify and avoid predatory journals — if the revision fails, choose the next journal with care.
• From MD/MS thesis to journal article — if the underlying work is a thesis, this conversion guide may save you a round of review.

Reviewer comments are advice, not instructions. Every substantive change must remain consistent with your data, your ethics approval and any registered protocol, and the final scientific decisions rest with the named authors.

If a major revision lands in the middle of clinical or laboratory work, our reporting-guideline review and revision support maps every comment to a concrete change so you can respond from evidence rather than memory, typically within 10–14 working days.