Respond to peer reviewer comments by answering each point, explaining the action you took, and identifying where the revised manuscript shows it. When you disagree or cannot complete a request, give a specific reason and explain what that means for the paper. The response letter and manuscript should tell the same story.
This guide includes a revision worksheet, a worked example, and a response-letter template. The examples are hypothetical teaching materials, not excerpts from an actual review or published study.
Read the decision letter before planning the revision
Start with the editor’s instructions, including the requested files, revision deadline, and any priorities or constraints. Use the journal’s requirements to decide how to present your response. If you need clarification about incompatible requests, identify the specific conflict when contacting the editor.
Nature’s guide to writing a reviewer response recommends a concise overview followed by replies to individual comments. It also asks authors to address issues specifically highlighted by the editor.
Before drafting polished replies, make a working copy of the decision letter and reviews. Keep the original comments intact. In your private planning notes, separate the scientific question from the action you think it requires. “The evidence does not support this conclusion” may require a narrower claim, further analysis, or both; changing the tone of a sentence alone may not resolve it.
Build a comment-to-change worksheet
Frontiers’ author guidance recommends organizing comments by reviewer or editor and tackling substantial revisions before cosmetic edits. Use the worksheet below to make your own revision plan visible.
| Comment ID | Question to resolve | Planned action | Completion evidence |
|---|---|---|---|
| R1.1 | Does the conclusion overstate what an observational design can establish? | Review the claim against the design and revise its wording where needed. | Final wording in the abstract, discussion, and conclusion; matching response. |
| R1.2 | Can readers understand how participants were recruited? | Check the study records and clarify the methods using documented details. | Revised recruitment paragraph and its final location. |
| R2.1 | Has a relevant alternative explanation been considered? | Evaluate the explanation and supporting literature before deciding how to revise. | Reasoned response, any resulting manuscript change, and checked sources. |
These rows describe possible tasks, not work that has already happened. Add an owner and status to your own copy. Useful statuses are “needs discussion,” “in progress,” and “checked against final draft.” Do not mark a comment complete just because a reply has been typed.
Use stable identifiers such as R1.1 throughout your notes. One comment may contain two requests: clarify a measure and justify its use, for example. Track both tasks while preserving the complete comment in the response letter.
Answer with a decision, an action, and a location
William Stafford Noble’s PLOS Computational Biology editorial on responding to reviewers advises giving a direct answer and distinguishing newly changed text from material that was already present. It also emphasizes addressing every point raised.
For your working draft, use three prompts: What is our answer? What actually changed? Where can the reviewer check it? If nothing changed, explain why. A reply such as “Addressed” leaves the reviewer to reconstruct your decision.
Presentation requirements differ. Noble recommends making replies self-contained, including revised wording where useful. Nature’s guide instead favors precise manuscript locations over reproducing blocks of text or figures. Follow your target journal’s instructions. Specify whether any page and line references refer to the revised manuscript.
Worked example: align a reply with an actual revision
Imagine a hypothetical observational study about study-space use. For this example only, assume the authors measured reported preferences and study-space use but did not establish a causal effect. The following reviewer comment and manuscript sentences are invented.
Reviewer comment R1.1:
The conclusion describes an improvement caused by the program, but the observational design does not establish causality. Please revise the claim and explain this limitation.
Original manuscript wording:
The program improved students’ use of study spaces.
Possible revised wording, only if supported by the study’s actual findings:
Program participation was associated with reported study-space use. The observational design does not establish whether participation caused the observed difference.
Example reply, written after those edits have been made and checked:
We agree that the original conclusion implied a causal effect that the study design cannot establish. We have replaced the causal wording with an association statement and added an explicit design limitation. We also checked the abstract and discussion for the same overstatement. The changes appear in the revised Conclusion, paragraph [number], and Discussion, paragraph [number].
The bracketed locations must be replaced before sending. The statement about checking the abstract and discussion must also be true. If those sections contain the same claim, change them as needed and identify their locations too.
This reply is useful because it names the interpretive problem and connects it to a manuscript change. It would be misleading to use it if the authors had only revised the letter, or if the data did not support an association in the first place.
When you disagree or cannot complete a request
Frontiers advises explaining disagreement constructively and giving a reason when a requested change is not feasible. Apply that principle to the specific scientific issue instead of replying with a bare “outside the scope.”
Suppose a reviewer asks the hypothetical study’s authors to examine long-term outcomes, but the study has no follow-up observations. An honest reply could be:
We understand the concern about whether the finding persists over time. The study collected observations at one time point and has no follow-up measurements, so these data cannot answer that question. We have limited the conclusion to the observed period and added the absence of follow-up as a limitation in [revised location]. We have not performed a longitudinal analysis.
Use that wording only when it describes the actual design and completed revision. Naming a limitation does not automatically resolve the reviewer’s concern: the editor may still consider additional evidence necessary. Keep the unresolved question visible rather than suggesting that a new paragraph supplies missing data.
When disagreement depends on literature, open and read the sources you cite. Our citation-checking guide separates verifying a reference from checking whether it supports the claim you want to make.
Copy this response-letter template
This is an adaptable structure, not a journal-specific form. Replace every placeholder, remove instructions, and match the editor’s requested format.
Manuscript: [Title and manuscript ID]
Revision: [Version/date]
Dear [Editor],
Thank you for the comments on our manuscript.
The principal changes in this revision are:
- [Completed change and the concern it addresses]
- [Completed change and the concern it addresses]
[State which manuscript version the locations below refer to.]
EDITOR COMMENT E1
[Complete comment]
Response: [Direct answer, completed action or reason for no change]
Location: [Section and final page/line or paragraph]
REVIEWER 1, COMMENT R1.1
[Complete comment]
Response: [Direct answer]
Change made: [What changed, or why no change was made]
Location: [Section and final page/line or paragraph]
[Revised wording, only if useful and allowed by the journal]
[Repeat for every remaining point and reviewer.]
Sincerely,
[Corresponding author, with coauthor agreement]Check the letter against the final manuscript
Read each reply beside the version you intend to upload. Our suggested final check is:
- Every comment identifier has a response, including comments with multiple requests.
- Statements such as “we added,” “we analyzed,” and “we corrected” describe completed work.
- Locations point to the final version, and quoted wording matches it.
- A change to a central claim is reflected wherever that claim appears.
- Any unresolved request has an explicit explanation rather than an empty reply.
- The required files and markup follow the decision letter and journal instructions.
If you use AI assistance, follow the applicable journal and institutional rules, including any confidentiality and disclosure requirements. In towrite.ai, proposed edits to your draft can be reviewed and accepted or rejected. You still need to verify that each retained edit answers the comment and preserves the meaning of your research.
Try towrite.ai on your draft as you work through revisions. Keep the response worksheet alongside the manuscript so that the letter describes the changes you actually chose to keep.
Prepared with AI assistance for towrite.ai. The study, review comments, and responses above are hypothetical teaching examples, not research findings or a real peer-review exchange. Publisher guidance was consulted on October 27, 2026.