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Response to Reviewers Letter Template

A response letter, cover note and manuscript note, plus sheets that split every reviewer comment into requests, each with a decision and line number.

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What you get

Pack of 6 files: 3 documents, 3 spreadsheets

Response to Reviewers Letter Template
  • Request RegisterSpreadsheet
  • Response LetterDocument
  • Disagreement LogSpreadsheet
  • Revised Manuscript NoteDocument
  • Conflict and Overlap MapSpreadsheet
  • Editor Cover NoteDocument
RiverResponse to Reviewers Letter Template

Request Register

Reviewer 3, comment 4. One number, five requests.

RowWhat it asks forKindIn the comment-by-comment draftDisposition
3.4aCounts are pooled across transects, ignoring the nesting structureAnalysisAnsweredMade
3.4bUnclear whether the counts are overdispersed, and if so Poisson is wrongAnalysisMissing, second sentenceMade
3.4cFigure 3 is unreadable at print size and its legend disagrees with Figure 2StructureMissing, parentheticalMade
3.4dThe four-week aggregation window needs justifyingReportingMissing, final sentenceMade in part
3.4eReplace the aggregation with a continuous time-varying termAnalysisMissing, final clauseDeclined

The draft written comment by comment answered comment 4 well and answered one fifth of it. Across three reports it answered all 24 comments and 33 of the 41 things they asked for.

How to write a response to reviewers

A response to reviewers, sometimes called a rebuttal letter, is the document you send with your revised manuscript, answering every point the editor and reviewers raised. For each one, quote it and say whether you made the change, made part of it or declined it. Then show what changed and where it now sits in the revised file, by page and line. A good one lets every reviewer check each answer without searching the manuscript.

The rule that matters most is to answer requests, not numbers. One numbered comment can hold two or three separate requests, and a reply that answers only the first leaves the rest open for the next round.

A hand ticks off items on a handwritten checklist in a notebook with a black pen
Turn the reports into a list of requests, then tick off each one. Photo: Jakub Żerdzicki on Unsplash

Read everything before you reply

Start with the editor's letter. It gives the decision and the deadline, and the editor's own comments need answers too. Then read every report through once before drafting a word.

Expect to feel stung, and don't answer in that mood. William Stafford Noble of the University of Washington, in his 2017 rules for responding to reviewers, suggests writing a venting version first1 and starting the real one several days later. Revision is the normal route to print: only 3.2% of the research papers Nature Neuroscience published in 20102 were accepted after a single round of review.

If a request would take months of new work, ask the editor whether it is essential. Nature Chemistry's editors say they are available to help authors pick out the deal-breakers from the polite suggestions3.

Split each comment into separate requests

Reviewers number their comments, but they write each one as prose. Noble names unanswered points as a frequent complaint from reviewers1 and notes that a single bullet can hold two separate issues, each needing its own reply.

So before answering anything, list each request on its own line, numbered by reviewer, comment and part (2.3a, 2.3b), and copy the reviewer's words exactly. A 2013 editorial in Nature Methods calls rephrasing a comment into a statement the author finds palatable4 a manipulative tactic, and a summary can do that by accident. Anything a reviewer could later say you ignored counts as a request, including:

  • An analysis to run, or to run differently
  • A number, definition or method detail to report
  • A claim to soften, support or cut
  • A table, figure or section to move, shorten or redraw
  • A question, even one with no instruction attached
ExampleOne comment, four requestsAn illustrative example written for this guide.

Reviewer 3, comment 4: "Counts are pooled across transects, which ignores the nesting structure; add a random intercept. It is also unclear whether the counts are overdispersed. (Figure 3 is unreadable at print size.) The four-week window needs some justification."

3.4a, analysis: "add a random intercept"

3.4b, question: "unclear whether the counts are overdispersed"

3.4c, figure: "Figure 3 is unreadable at print size"

3.4d, reporting: "The four-week window needs some justification"

  • Four rows, one number. Answered in one block, 3.4b to 3.4d are easy to skip, especially the aside in parentheses.

Decide what to do with each request

Give every request one of three answers: made, made in part, or declined. Avoid "addressed", which hides which of the three you mean. Noble calls the stock reply "this point is addressed in the manuscript" a common error, since the reader can't tell whether anything changed.

Made in part is a respectable answer: say what you did, what you didn't, and why. Declining is acceptable too, given a reason the editor can weigh and, ideally, a smaller change instead. Nature Chemistry's editors expect authors who skip a requested experiment or analysis to provide a compelling argument3 that their conclusions stand without it.

When declining is credible

ReasonWhat makes it credible
Already in the paperQuote the passage and make it easier to find, since other readers may miss it too.
Not supported by the dataSay exactly why the analysis can't be run or wouldn't show what the reviewer expects.
Needs new dataName what you would have to collect and how long it would take.
Contradicted by the literatureCite the study that answers the point directly, not several nearby ones.
Outside the paper's questionCredible only if your introduction states the question narrowly and early.

"Beyond the scope" needs a reason

Noble warns that if a reviewer asks for 10 things and you call 9 of them out of scope, you are not likely to satisfy the reviewer.

When reviewers disagree, tell the editor

Before drafting, run your list of requests against itself. Where two reviewers ask for the same change, make it once and answer it under each of them. Where they want opposite things, don't quietly pick a side.

Assume every reviewer reads the whole letter. Nature Portfolio journals share each referee report with the other reviewers5 and may ask them to comment on one another's criticisms. The same policy says editors weigh the reviewers' and authors' arguments rather than counting votes.

Hand the conflict to the editor in your cover letter. Nature Chemistry's editors call that letter the place for anything the editor should be aware of3 that you might not raise with the referees. Say what each reviewer asked, which way you went and why, and never play one reviewer against the other.

Structure the response letter

Noble recommends opening with a summary of the changes1, then the complete reviews with your answers between the comments. Keep the thanks to one line at the top. Go reviewer by reviewer in their numbering, answering each comment's parts under their own labels: 4.1, 4.2, 4.3.

Begin every answer with what you did: Noble advises a direct answer first, a yes or no where possible, with background after it. Then quote the new text and give its page and line, saying whether they refer to the marked-up or the clean copy.

ExampleOne answer, done wellAn illustrative example written for this guide.

Comment 4, second sentence: "It is also unclear whether the counts are overdispersed."

Response 4.2, made. We tested for overdispersion and found it. Methods, page 10, lines 242 to 249 of the marked-up copy, now reads: "Because the counts were overdispersed, all models use a negative binomial family."

  • Decision first. "Made" comes before any explanation, so a reviewer skimming for the outcome finds it.
  • Not this. "We thank the reviewer for this valuable comment, which has been addressed" says neither what changed nor where.

Flag any change nobody asked for, such as a corrected error. If an analysis changed, report what it returned even when the result got weaker, and make the methods match. A statistical methods section written from your analysis script keeps the two in step.

Write the letter as if it will be public, because it may be. If you opt in at PLOS One, your response to reviewers appears online alongside the article6, and Nature Portfolio's transparent peer review files can include author rebuttal letters.

Check the package before you resubmit

Line numbers move whenever text is added above them, so confirm every location last, in the final file. Then read the letter against your list of requests, not the reviewers' numbering.

The decision letter or author guide names the files to upload. PLOS One, for example, asks for a response to reviewers file plus marked-up and clean copies6 of the manuscript. Run any citation you added through a citation and reference check before uploading.

Before you resubmit

  • Every request is marked made, made in part or declined
  • Every change has a page and line, checked in the final file
  • Every decline gives a reason and the evidence behind it
  • Conflicts between reviewers are explained in the cover letter
  • Changes nobody asked for are listed
  • The files match what the journal asked for

The template at the top of this page is built this way. Its Request Register gives every request a row, and its Disagreement Log and Conflict and Overlap Map hold the declines and conflicts. Open it in River and it splits your reports into the register before any drafting starts.

How to use this template

Use the files as they are, or open them in River. River asks for your decision letter with every report, the manuscript and your deadline if you have one. Then it splits each numbered comment into the separate things it asks for and opens the Request Register with every request quoted word for word and labeled by kind.

It tells you how many comments and how many requests you have, how much of the work means rerunning analyses, and where reviewers ask for opposite things. It doesn't draft replies yet, and it won't suggest what to decline, since that call is yours. When you're ready, it helps fill in changes and locations, argue declines, and write the letter and cover note. Nothing reaches the journal until you upload it.

  1. Download it or open it in River

    Get the three Word documents and three CSV sheets free, or open the template in River and send it your reports.

  2. Split the reports into requests

    Give each separate request its own row in the Request Register, quoted word for word, or let River split them.

  3. Decide, change and locate

    Mark each request made, made in part or declined, then record the change and its page and line in the revised file.

  4. Write the letter and resubmit

    Draft the response and the editor's cover note from the register, run the final check, and upload what the journal asks for.

What's in the template

Every sheet in the packThe Request Register, the two joins that run across it, and the letter written from all three.
Response to Reviewers Letter Template
RiverRequest Register

Request Register

41 rows, one per request, against 24 numbered comments. The column that does the work is the last one: a response with no location is a response an editor has to take on trust.

RowThe requestDispositionChange madeLocation in the revised fileAlso answers
1.1aA decline in verge-nesting species is asserted without a sourceMadeCited to the 2024 monitoring report with the interval, not the direction aloneIntro p.3 L62-66
1.2aWas the 2019 season excluded, and if so whyMade2019 included in the primary analysis, exclusion criteria statedMethods p.8 L176-1902.3a, 3.3a
3.4aCounts pooled across transects, ignoring the nesting structureMadeRandom intercept added, the estimate falls from 1.34 to 1.19 and both are reportedMethods p.10 L228-241
3.4eReplace the aggregation with a continuous time-varying termDeclinedFixed four-week rota leaves no within-window variation to estimate fromLimitations p.19 L452-459
2.6bAt least characterize adjacent land use if you cannot model itMadeLand use within 250 m tabulated per siteSupp. Table S7

Row 1.2a is one edit that answers three reviewers. It appears in the letter three times, under each of them, rather than once with a pointer.

RiverConflict and Overlap Map

Conflict and Overlap Map

The register run against itself. Two reviewers asking for opposite things is the editor's decision, and an author who settles it quietly has told the losing reviewer nothing.

KindRowsOne asksThe other asksResolutionTo the editor
Conflict1.3a / 3.6aCut the sensitivity analyses for lengthAdd two moreTwo added, all six moved to supplementary, main text shorter than beforeYes
Conflict2.2a / 3.5aMove Table 2 to supplementaryExpand Table 2 with the per-taxon breakdownKept and expanded, the other request declined with the conflict namedYes
Overlap1.2a / 2.3a / 3.3aWhy was 2019 excludedSame question, three phrasingsOne change, cross-referenced under all threeNoted
Overlap1.4a / 2.7c / 3.7aThe abstract overstates the designCausal language is not earnedNarrowing the abstract and the discussion answers all threeNoted

Two conflicts and four shared changes out of 41 requests. Both conflicts went into the cover note, where they read as a decision explained rather than a problem discovered.

RiverDisagreement Log

Disagreement Log

Six declines, each with a reason class and the evidence it rests on. The last column is the test: write the reviewer's best comeback, and if it comes easily the decline is not finished.

RowThe requestReason classWhat it rests onDone insteadTheir strongest reply
3.4eContinuous time-varying termNot supported by the dataSurvey visits were on a fixed four-week rotaTwo-week window reported as a sensitivity analysisIt would still absorb seasonal trend
2.5aLandscape floral resource covariateWould require new data collectionCosted at one season, three observersNamed as a confounder with the likely direction of biasA remotely sensed proxy could substitute
2.2aMove Table 2 to supplementaryOutside the question the paper asksReviewer 3 asks for the same table to be expandedKept and expanded, conflict handed to the editorThe paper is long and something has to move
3.7bReframe the analysis causallyContradicted by the literatureAssignment follows road class, which also predicts the outcomeCausal framing dropped rather than reframedThen the paper says less

Row 2.2a is the only decline resting on a scope boundary, which is the weakest class there is. It is also the one the cover note asks the editor to rule on rather than settling.

RiverResponse Letter

Response Letter

Written in the reviewer's numbering, because that is what they will read it in. Underneath it, each part answered separately and labeled, so a reviewer can see their second sentence was read.

ElementWhat goes in it
OpeningThanks once. Then the count: 24 comments, 41 requests, 30 made, 5 made in part, 6 declined.
Summary of changesFour to six substantive ones, so a reader who stops here knows what happened to the paper.
The change nobody asked forA transcription error found while rebuilding the analysis, disclosed in the opening rather than left to be noticed.
Response 4.1, madeDisposition, then the change, then the location. Never the other way around.
Response 4.2 to 4.5The four requests a single response under comment 4 would have swallowed, each answered under its own label.
Response 4.5, declinedReason class, the evidence, and the smaller change made instead. Never a bare scope assertion.

Reviewer 3 recommended rejection, and their eight comments hold 16 requests, more than either colleague. Those are the rows that decide the paper, so they get answered at the same depth as everything else.

  • Request Register sheetEvery request on its own row, quoted word for word, with its kind, decision, change and location.
  • Response LetterThe letter in each reviewer's numbering, with every part of a comment answered under its own label.
  • Disagreement Log sheetEach declined request with its reason, the evidence, what you did instead and the reviewer's strongest reply.
  • Revised Manuscript NoteWhat the resubmission contains, how much of the manuscript changed and any correction nobody asked for.
  • Conflict and Overlap Map sheetWhere two reviewers want opposite things, and where one change answers more than one of them.
  • Editor Cover NoteUnder a page for the editor: what changed, the counts, the conflicts and one line per decline.

Common questions

What should a response to reviewers letter include?

A brief note to the editor, a summary of the main changes, and every reviewer comment quoted in full with your reply beneath it. Each reply gives your decision (made, made in part or declined), the change itself, and its page and line in the revised manuscript.

How long should a response to reviewers be?

As long as it takes to answer every request, with each answer kept short: the decision, the change and its location. Quote short changes in full, but for a long new section give its title and location rather than pasting it in. A major revision with dozens of requests can still run to many pages.

Can you disagree with a reviewer?

Yes, as long as you give a reason and the evidence behind it. Say what kind of reason it is, such as needing new data or falling outside the paper's question, and offer a smaller change where you can. A bare "beyond the scope of this study" gives the editor nothing to weigh.

What if two reviewers ask for opposite things?

Take the conflict to the editor, who makes the final call. Describe it in your cover letter, explain the choice you made, and answer both reviewers in the response itself. At some journals, including Nature Portfolio titles, reviewers see each other's reports, so assume both will read your decision.

Is this response to reviewers template free?

Yes. Download the three Word documents and three CSV sheets with no signup. They come filled in with a made-up field study whose 24 reviewer comments split into 41 requests, so you can see how the parts fit before replacing them. Edit with AI opens the same template in a free River workspace.

What does Edit with AI do?

It opens the template in a free River workspace and asks for your decision letter, every report and the manuscript. River splits each numbered comment into its separate requests, fills the Request Register and tells you how many requests you really have. It flags conflicts between reviewers. What to change or decline stays your call.

Sources

  1. PLOS Computational Biology. “Ten simple rules for writing a response to reviewers.” journals.plos.org (opens in a new tab)

  2. Nature Neuroscience. “Crafting a revision.” nature.com (opens in a new tab)

  3. Nature Chemistry. “Revision notes.” nature.com (opens in a new tab)

  4. Nature Methods. “The way you say it.” nature.com (opens in a new tab)

  5. Nature Portfolio. “Peer Review.” nature.com (opens in a new tab)

  6. PLOS One. “Revising Your Manuscript.” journals.plos.org (opens in a new tab)

Written by

Chandler Supple

Co-founder & CEO, River

Chandler has spent the last six years working in AI, building tools for millions of users and Fortune 100 companies. In 2025, he co-founded River to build a new kind of operating system for AI agents.

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Reviewed by

Brian Joseff, Co-founder, River

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