Quote each reviewer comment, answer point by point, mark edits, justify choices with citations, and keep a respectful, precise tone.
Peer review can reshape a study, but the path runs smoother when authors reply with clarity and grace. This guide shows how to write a response that helps editors, satisfies reviewers, and strengthens the science. You’ll see structure, phrasing, and file prep that fit medical journals. Nothing flashy—just clean, repeatable steps.
Commenting On Peer Review For A Medical Manuscript: Step-By-Step
Start With A Calm Overview
Open with thanks to the editor and all reviewers. State that you revised the manuscript, list the main areas you improved, and name the files you’re submitting. Keep this section short and specific so an editor can scan it in seconds.
Set Up A Response Document
Create a separate file titled “Response to Reviewers.” Paste every comment in full. Number them by reviewer and line. After each quoted comment, write “Response:” on a new line and give your answer. Use plain text, not fancy styles. In the revised manuscript, switch on tracked changes or mark edits so the reader can spot them fast.
Triage The Comments
Group notes into three buckets: major, moderate, and minor. Major notes change claims, methods, or analyses. Moderate notes tune framing, clarity, or small methods gaps. Minor notes fix style, labels, typos, or small references. Draft replies in the same order the journal letter uses so no item goes missing.
| Reviewer Comment Type | What It Signals | Best Response Move |
|---|---|---|
| Requests for new analyses | Concern about strength or missing tests | Run the analysis or explain limits; report exact models and outputs |
| Clarification on methods | Procedures or variables aren’t clear | Add detail, units, time windows, and references; cite checklists if relevant |
| Sample size or power | Uncertain precision or risk of error | Provide power logic, CIs, and sensitivity checks; adjust claims if needed |
| Ethics or registration | Compliance or transparency gaps | State approvals, consent, and registry IDs; add missing details |
| Conflicting literature | Context may be incomplete | Add balanced citations and explain where your data fit |
Keep The Paper Aligned With Core Rules
Editors expect basic standards. Align the file with widely used instructions such as the ICMJE Recommendations. Match your study design to a reporting checklist from the EQUATOR reporting guidelines library. When a reviewer flags a gap that maps to a checklist item, say so and show the fix.
Writing Responses To Peer Review For A Medical Paper
Match Each Comment With A Direct Answer
Quote the reviewer, then answer in one tight paragraph before any long detail. Lead with agreement where you can. If the request is broad, break your answer into indented bullets so changes stand out. Close each item with a pointer to the manuscript page and line numbers.
Show The Exact Change
Reviewers want proof. After your short answer, paste the revised sentence or paragraph in quotation marks. If the change touches several sections, show the most visible one and list the others with page and line numbers. Keep quotes from the manuscript in plain text to avoid markup glitches in submission systems.
Disagree Without Friction
Sometimes a request doesn’t fit your data or scope. Say so without heat. A clear path is to thank the reviewer, give a brief rationale, offer a smaller step that still adds clarity, and show where you’ve updated the text to reflect that limit. Avoid sweeping claims; stick to what your data can carry.
Back Claims With Evidence
When a reviewer challenges a citation, method, or interpretation, answer with specific evidence. Add high-quality references, show main numbers, and avoid vague phrases. If the change shifts the message, adjust the abstract and title lines so they match the new shape of the paper.
Signal Reporting Rigor
Many comments mirror items from well known checklists. Point to the item and confirm the fix. For syntheses, link to the PRISMA 2020 checklist. For trials, mark text that states allocation, masking, and flow. For observational work, name variables and handling of missing data. Clear links between comments and reporting items save time for everyone.
Tone, Clarity, And Reader Trust
Use Respectful Language
Keep replies professional even when feedback feels sharp. Avoid sarcasm or loaded terms. If a note repeats content already in the paper, assume the text wasn’t clear and fix the paper not the reviewer.
Keep Sentences Tight
Short sentences reduce misreadings. Cut double hedges and filler. Use active verbs: “We re-ran the model including age and sex” lands better than a long passive line.
Avoid Defensive Framing
Skip phrases that sound combative. Replace “We strongly disagree” with “Our data don’t support that pattern.” Replace “As we already stated” with “We’ve clarified this point in Results, page 7.”
Credit Reviewers
When a suggestion lifts the paper, say so. A quick note such as “We adopted this and it sharpened the message” builds rapport and shows care for the science, not just the decision.
Structure That Editors Love
Editor Letter Snapshot
Write an editor letter to the editor that lists the number of major and minor changes, the added analyses, and any limits you couldn’t resolve. If you moved text between sections, note that too. Keep it to one page.
Point-By-Point File Works
The response file carries the weight. Use clear headings: “Reviewer 1,” “Reviewer 2,” and so on. Under each, keep the quote-answer-evidence flow. Insert page and line pointers every time you claim a change.
Marked Manuscript
Use tracked changes or colored marks in the revised manuscript. Don’t hide deletions. If the journal bans tracked changes, use yellow shading on new text and strikethrough in a PDF to show removals. Consistent signals stop confusion.
Clean Manuscript
Also provide a clean copy. Editors share this with production if accepted, so fix spacing, figure labels, and abbreviations. Make sure tables and figures match the text and that legends stand on their own.
Data And Supplement
Update data citations, code links, and preregistration details. Move checklists, protocols, and extended tables to the supplement when allowed. Cross-link each item from the response so a reader can click straight to proof.
Handling Tough Requests
New Analyses
Run new tests when they’re feasible and relevant. Report model terms, software, versions, and settings. If the analysis was already tried, say so and include results in the supplement. If power is thin, say so and temper claims.
New Experiments
Sometimes a reviewer asks for a new study. If the time or cost would stall progress, explain constraints and outline follow-on studies while tightening claims in the current paper. Expand the limits section and add data that bracket the concern, such as sensitivity checks or simulations.
Out Of Scope Requests
When a request drifts outside your question, anchor your reply to the study aim. Offer a short paragraph in the discussion that sets boundaries and points readers to work that targets the side topic. Keep the main thread intact.
Conflicting Reviews
If Reviewer 1 and Reviewer 2 pull in opposite directions, flag this for the editor in a courteous note. Propose a path that meets the journal’s audience and the data. Show how the revised text meets both where possible.
| Study Type | Checklist Touchpoints | Typical Fixes After Review |
|---|---|---|
| Randomized trial | CONSORT items on allocation, masking, flow | Add allocation ratio, concealment steps, and a full flow diagram |
| Systematic review | PRISMA items on search, selection, and synthesis | Expand search strings, add a selection figure, and detail synthesis rules |
| Observational study | Common EQUATOR items on variables and bias | Define exposures, outcomes, and bias handling; show missing data logic |
Quality Check Before Resubmission
Run A Self-Audit
Confirm every comment received a reply and a change where warranted. Test all internal links, figure calls, and references. Read the abstract last to ensure it mirrors the revised results and the tighter message.
Polish Presentation
Fix style in tables and figures. Use consistent decimals, consistent units, and clear axis labels. Keep titles factual. If new data changed a main number, update figure text and the abstract as well.
Micro-Phrases That Defuse Tension
These short lines keep replies crisp and civil:
- “Thank you for this helpful point. We’ve revised the text on page 5 to clarify.”
- “We agree and have added the requested analysis; results appear on page 9.”
- “Our data set can’t support that test; we’ve narrowed the claim and explained the limit.”
- “We’ve added citations to recent studies that report a related effect.”
- “We ran a sensitivity check; it didn’t change the estimate and is now in the supplement.”
- “We misunderstood the question at first; thanks for catching this. The revision fixes it.”
Common Pitfalls To Avoid
- Skipping a comment or merging several into one reply
- Letting tone drift into frustration or sarcasm
- Padding the response with long quotes from the manuscript instead of a direct answer
- Moving new results into the paper without updating the abstract and title
- Ignoring journal-specific file names and upload rules
- Sending only a clean copy when the journal asked for a marked file
Sample Paragraphs You Can Adapt
When You Agree
Reviewer 2, Comment 3: Please report how missing data were handled in the primary model.
Response: Thank you for flagging this gap. We now state that missing covariates were handled with multiple imputation using chained equations (five imputations; Rubin’s rules), and we added a complete-case check. See Methods, page 6, lines 112–128.
When You Partly Agree
Reviewer 1, Comment 5: Include BMI in every model.
Response: We share the concern. BMI correlates with exposure and outcome in this cohort, but it sits on the causal chain for part of the effect. We now present models with and without BMI and moved the causal diagram to the supplement. See Results, page 8, and Figure S2.
When You Disagree
Reviewer 3, Comment 2: Conclude that treatment A is better than B in all subgroups.
Response: Our data don’t support a broad claim across subgroups. Power falls in several strata and estimates vary. We now limit the statement to the primary outcome and note subgroup trends as exploratory. See Discussion, page 12.
When Requests Conflict
Reviewer 1, Comment 1: Compress the methods.
Reviewer 2, Comment 4: Add full assay detail.Response: We kept a concise core in the main text and moved assay steps, kit numbers, and validation to the supplement. The main text now cross-refers to Supplementary Methods, pages S2–S4.
Preparing Data, Code, And Materials
Data Access Notes
Spell out what can be shared and under what terms. If data are public, give the repository, accession numbers, and a stable link. If data are controlled, write one clear sentence on who holds custody and how qualified researchers can request access. Add a short data dictionary in the supplement so reviewers can read variable names without digging through code.
Code And Reproducibility
Post scripts with readme files that tell someone how to run them from start to finish. Pin package versions. Set seeds for any random steps.
Materials And Protocols
For lab work, list catalog numbers, vendors, and lot numbers when available. If a step needed pilot tuning, write down what finally worked and the range you tried. If a kit or instrument changed mid-study, note the dates and any cross-validation you ran to show consistency.
Submission Portal Tips
File Names That Help Editors
Use names that sort well and tell the story: “Cover_Letter.pdf,” “Response_To_Reviewers.pdf,” “Manuscript_Marked.docx,” “Manuscript_Clean.docx,” “Figures.zip,” and “Supplement.pdf.” If the system strips spaces, use underscores. Avoid version chaos by keeping one master folder and a change log.
Final Sanity Pass
Log into the portal before the deadline and preview every file as a reader would. Check that tables render, figures show crisp text, and hyperlinks work. Confirm that the response file mirrors every change in the manuscript.
Treat the exchange as a collaboration. Clear, courteous replies help editors make quick decisions and help readers trust the final paper. With a tidy structure, honest limits, and precise text, your response file does real work long before the acceptance email arrives.