When to Say 'We Respectfully Disagree'

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-28

Quick Answer

• Decide based on comment type, evidence strength, and journal policy, not on emotion or fear of rejection.
• Accept comments that request clarity, reporting completeness, or minor corrections, prepare a firm, evidence-backed disagreement only for comments that misread your data or demand unsupported changes.
• A respectful disagreement still requires a detailed point-by-point response letter, and the editor holds final authority on whether your rebuttal is accepted.

Understanding the Reviewer Comment Landscape

Peer review exists to improve manuscripts before publication. The Committee on Publication Ethics Core Practices describe peer review as a process where journals rely on reviewers to assess the validity and quality of submitted work, and where journals should provide authors with clear guidance on the process. When you receive a decision letter with reviewer comments, you are not obligated to accept every suggestion. You are obligated to respond to every comment, and to do so with evidence and professional courtesy.

The practical problem for most authors is not whether they can disagree. It is whether they should. A poorly chosen disagreement can delay publication, create editorial friction, or result in rejection. A poorly chosen acceptance can weaken your paper, introduce errors, or compromise the integrity of your findings. The decision tree in this article helps you sort comments into categories and apply a consistent decision process.

At a Glance

The table below summarizes the main comment categories and the recommended response strategy for each.

Core Principles for Deciding When to Disagree

The Editor Is Your Primary Audience

Your response letter is read by the editor first, and the editor decides whether to send the revision back to the original reviewers or make a decision themselves. The Committee on Publication Ethics Core Practices state that journals should have a defined process for handling complaints about peer review, and that editors should act on concerns about review quality. This means the editor is not simply a messenger. The editor is the decision maker who weighs your rebuttal against the reviewer's original concern.

When you write a disagreement, you are writing to the editor, not to the reviewer. Your goal is to show the editor that you have considered the comment seriously, that you have evidence to support your position, and that your decision is reasonable. A response that reads as defensive or dismissive will not help you.

The Three Question Test

Before you draft any response, run the comment through three questions.

First, is the comment factually correct? If the reviewer says your sample size is 20 when it is 25, the comment is correct and you should fix the error. If the reviewer says your sample size is 20 when it is 25, and the reviewer misread the table, you can disagree with the correction and point to the correct table.

Second, is the comment within the scope of the study? A reviewer who asks you to add a new clinical outcome that you never measured is asking for something outside the scope. A reviewer who asks you to report the confidence intervals for the outcomes you did measure is asking for something within the scope.

Third, is the comment feasible? A reviewer who asks you to collect new data from a cohort that no longer exists is asking for something infeasible. A reviewer who asks you to reanalyze existing data with a different statistical method is asking for something feasible.

These three questions do not always align. A comment can be factually correct but outside the scope. A comment can be within the scope but infeasible. The decision tree in the next section helps you weigh these factors.

The Decision Tree for Reviewer Comments

The following flowchart shows the decision path for a single reviewer comment. Use it for each comment in the decision letter, one at a time.

flowchart TD
    A[Reviewer comment received] --> B{Is the comment factually correct?}
    B -->|Yes| C[Accept the comment and revise the manuscript]
    B -->|No| D{Is the comment within the study scope?}
    D -->|Yes| E{Is the requested change feasible?}
    D -->|No| F[Prepare a respectful disagreement with evidence]
    E -->|Yes| G[Accept the comment and revise the manuscript]
    E -->|No| H[Prepare a respectful disagreement with feasibility rationale]
    F --> I[Send response letter to editor]
    H --> I
    C --> I

The flowchart shows that factual correctness is the first gate. If the comment is correct, you accept it. If the comment is not correct, you then ask whether it is within the scope of the study. If it is within scope and feasible, you accept it. If it is within scope but not feasible, or if it is outside scope entirely, you prepare a disagreement.

When the Comment Is Factually Correct

A factually correct comment is one where the reviewer has identified an error in your manuscript. This includes errors in numbers, citations, statistical results, figure labels, or descriptions of your methods. The correct response is to accept the comment, fix the error, and thank the reviewer in your response letter.

There is no strategic advantage to disagreeing with a correct comment. The editor will see the error, and your disagreement will appear unreasonable. Even if the error is minor, the professional response is to acknowledge it and correct it.

When the Comment Is Factually Incorrect

A factually incorrect comment is one where the reviewer has misread your manuscript, misunderstood your methods, or made an error in their own reasoning. This is the category where a respectful disagreement is appropriate.

The key word is respectful. Your response letter should state that you disagree, explain why, and provide the evidence from your manuscript or your data that supports your position. You should not accuse the reviewer of being careless or incompetent. You should simply show the editor the facts.

When the Comment Is Within Scope but Infeasible

A comment can be within the scope of your study but infeasible to implement. The most common example is a request for additional data collection. If your study is retrospective and the data no longer exist, you cannot collect them. If your study is prospective and the enrollment period has closed, you cannot add new participants.

In this case, you should explain the feasibility limitation in your response letter. You should also state what you have done instead, such as adding a limitation paragraph to the discussion or performing a sensitivity analysis with the existing data.

When the Comment Is Outside the Scope

A comment is outside the scope when it asks you to change the study design, add a new research question, or address a topic that your study was not designed to answer. The reviewer may be asking for a different study, not a revision of your study.

In this case, you can disagree with the comment and explain that the requested change is outside the scope of the current manuscript. You should also explain what the study does address, so the editor can see that the comment is not a valid criticism of the work.

How to Write a Respectful Disagreement

Structure of a Response Letter

A response letter is a point-by-point reply to each reviewer comment. The standard structure is to list each comment, then provide your response beneath it. For comments you accept, your response is a description of the change you made. For comments you disagree with, your response is a reasoned rebuttal.

The Committee on Publication Ethics Core Practices emphasize that journals should have a clear process for handling complaints about peer review. Your response letter is not a complaint. It is a professional communication. The same principles of clarity and transparency apply.

The Rebuttal Paragraph

A rebuttal paragraph should have three parts. First, acknowledge the reviewer's concern. Second, state your position. Third, provide the evidence.

An example of a rebuttal paragraph for a comment that misreads your statistical method:

"The reviewer is correct that the manuscript does not explicitly state the type of mixed-effects model used. We have added this information to the Methods section. However, the reviewer's statement that the model does not account for repeated measures is incorrect. The model includes a random intercept for each animal, which accounts for the repeated measures structure. We have clarified this in the revised manuscript."

This paragraph acknowledges the concern, states the position, and provides the evidence. It does not attack the reviewer. It does not use emotional language. It simply shows the editor that the reviewer's criticism is based on a misreading.

The Tone of the Response

The tone of your response letter should be professional and neutral. Avoid language that is defensive, sarcastic, or dismissive. Avoid phrases like "the reviewer clearly did not read the manuscript" or "this comment is without merit." Instead, use phrases like "we appreciate the reviewer's concern" and "we have clarified this point in the revised manuscript."

The editor is reading your response to decide whether the reviewer's concern is valid. If your response is professional and evidence-based, the editor is more likely to accept your position. If your response is emotional or dismissive, the editor may side with the reviewer even if the reviewer is wrong.

When to Accept a Comment Even If You Disagree

The Cost-Benefit Analysis

There are times when a comment is not factually correct, but the cost of disagreeing is higher than the cost of accepting. This is a strategic decision, and it is a legitimate one.

The cost of disagreeing includes the risk that the editor will side with the reviewer, the risk of a second round of review, and the risk of rejection. The cost of accepting includes the time to make the change and the potential impact on your manuscript.

For example, a reviewer may ask you to add a sentence to the discussion that you believe is not fully supported by your data. You can disagree, and you may be right. But if the sentence is not harmful, and if the reviewer is likely to be offended by a disagreement, the cost of accepting may be lower.

When to Accept a Comment That Is Not Factually Correct

Accept a comment that is not factually correct when the requested change is small, when it does not affect the conclusions of your study, and when the reviewer is likely to be sensitive to disagreement.

For example, a reviewer may ask you to describe your study as a "pilot study" when you believe it is a full study. You can disagree, but the label does not change the results. If the reviewer is the editor's trusted advisor, the cost of disagreeing may be higher than the cost of accepting.

When to Disagree Even If the Cost Is High

Disagree when the requested change would compromise the integrity of your study. This includes requests to remove data, to change your statistical analysis to a less appropriate method, or to make a claim that your data does not support.

The Committee on Publication Ethics Core Practices state that journals should have policies on data and reproducibility, and that authors should be prepared to provide their data to the journal. If a reviewer asks you to remove data that is valid, you should disagree. If a reviewer asks you to change your analysis to a method that is less appropriate, you should disagree.

The Role of Journal Policies and Funder Requirements

Journal Policies on Peer Review

The Committee on Publication Ethics Core Practices describe the responsibilities of editors and authors in the peer review process. Journals are expected to have clear policies on peer review, and authors are expected to follow those policies. Before you decide to disagree with a reviewer, check the journal's policies on the revision process.

Some journals have a policy that all reviewer comments must be addressed, but the author may disagree with a comment and explain why. Other journals have a policy that the author must accept all comments. The journal's policies are the first constraint on your decision.

Funder Requirements

If your research is funded by a government agency or a foundation, the funder may have requirements that affect your response to reviewer comments. The National Institutes of Health Grants and Funding pages describe the expectations for grant recipients, including the need to conduct research with integrity and to share data according to the NIH Data Management and Sharing Policy.

If a reviewer asks you to change your data management plan, and your funder requires a specific data sharing approach, you should align your response with the funder's requirements. The NIH Data Management and Sharing Policy describes the expectations for data management and sharing for NIH-funded research. If the reviewer's comment conflicts with the funder's policy, you should explain the conflict to the editor.

Reporting Guidelines

The EQUATOR Network provides a collection of reporting guidelines for different study types. If a reviewer asks you to follow a reporting guideline, and the guideline is appropriate for your study type, you should accept the comment. If the reviewer asks you to follow a guideline that is not appropriate for your study type, you can disagree and explain why the guideline does not apply.

For example, a reviewer may ask you to follow the CONSORT guideline for a randomized trial. If your study is a randomized trial, you should accept the comment. If your study is an observational study, you should explain that the CONSORT guideline does not apply and that you have followed the appropriate guideline, such as STROBE.

Practical Steps for Implementing Your Decision

Step 1: Read All Comments and Classify Them

Read the decision letter and all reviewer comments. Create a table with one row per comment. In the table, classify each comment as accept, disagree, or accept with modification. Use the decision tree in this article to guide your classification.

Step 2: Draft the Response Letter

Draft the response letter with a point-by-point structure. For each comment, write the reviewer's comment, then your response. For comments you accept, state the change you made. For comments you disagree with, state your position and provide the evidence.

Step 3: Check the Journal Policies

Before you submit the response, check the journal's policies on the revision process. Confirm that the journal allows authors to disagree with reviewer comments. Confirm that the journal has a specific format for the response letter.

Step 4: Submit the Response

Submit the response letter and the revised manuscript through the journal's submission system. Include a cover letter to the editor that summarizes your main decisions and highlights any disagreements.

Records and Measurements

What to Record

Keep a record of your decision for each reviewer comment. Record the comment, your classification, and your response. This record is useful if the manuscript goes through a second round of review, and it is useful if you need to explain your decisions to a coauthor or a supervisor.

What to Measure

Measure the number of comments you accepted versus the number you disagreed with. If you disagree with more than a third of the comments, you should review your decision process. A high disagreement rate may indicate that you are being too defensive, or that the reviewer is not a good fit for your manuscript.

What to Track Over Time

Track the outcome of your revisions. Did the editor accept your disagreements? Did the manuscript go through a second round of review? Did the manuscript get accepted? This information helps you calibrate your decision process for future submissions.

Common Failure Patterns

The Failure to Disagree

The most common failure is to accept every comment, even when the comment is wrong. This happens when the author is afraid of rejection. The result is a manuscript that is weakened by unnecessary changes, or a manuscript that contains errors introduced by the reviewer.

The Failure to Accept

The opposite failure is to disagree with every comment, even when the comment is correct. This happens when the author is defensive. The result is a response letter that is hostile, and the editor is likely to side with the reviewer.

The Failure to Provide Evidence

A third failure is to disagree without providing evidence. The author states that the reviewer is wrong, but does not explain why. The editor cannot evaluate the disagreement, and the response is likely to be rejected.

The Failure to Follow Journal Policy

A fourth failure is to disagree with a comment that the journal policy requires you to accept. For example, if the journal requires you to follow a specific reporting guideline, and you disagree with the reviewer's request to follow the guideline, the editor will reject your response.

Limitations and Professional Escalation

Limitations of the Decision Tree

The decision tree in this article is a guide, not a rule. It does not account for the specific context of your manuscript, the specific reviewer, or the specific journal. You should use the tree as a starting point and apply your own judgment.

When to Escalate

If you believe a reviewer comment is beyond wrong but also unethical, you should escalate the issue to the editor. The Committee on Publication Ethics Core Practices describe the responsibilities of authors and editors in handling misconduct. If a reviewer asks you to falsify data, or to remove data that is valid, you should report the issue to the editor.

When to Seek Advice

If you are unsure whether to disagree with a comment, seek advice from a coauthor, a mentor, or a colleague who has experience with the journal. A second opinion can help you see the comment from the editor's perspective.

Frequently Asked Questions

What is the difference between a disagreement and a complaint?

A disagreement is a response to a reviewer comment that you believe is incorrect. A complaint is a formal request to the editor about the review process. The Committee on Publication Ethics Core Practices describe the process for handling complaints about peer review. You should use a disagreement in your response letter, and you should use a complaint only if you believe the review process was unfair.

How do I respond to a reviewer who asks for a new analysis?

Assess whether the analysis is within the scope of your study and whether it is feasible. If the analysis is feasible and informative, accept the comment and add the analysis. If the analysis is not feasible, explain the feasibility constraint in your response. If the analysis is outside the scope, explain that the analysis is not part of the study design.

How do I respond to a reviewer who asks me to remove data?

If the data is valid and the removal would compromise the integrity of your study, disagree with the comment. Explain why the data is valid and why the removal would be inappropriate. The Committee on Publication Ethics Core Practices describe the importance of data integrity in the publication process.

How do I respond to a reviewer who asks me to change my conclusion?

Assess whether the reviewer's requested conclusion is supported by your data. If the reviewer's conclusion is supported, accept the comment and change the conclusion. If the reviewer's conclusion is not supported, disagree and explain why your original conclusion is the correct one.

How do I respond to a reviewer who asks me to follow a reporting guideline?

Check the EQUATOR Network to see if the guideline is appropriate for your study type. If the guideline is appropriate, accept the comment and follow the guideline. If the guideline is not appropriate, explain why the guideline does not apply to your study type.

How do I respond to a reviewer who asks me to share data?

Check the funder's data sharing policy. The NIH Data Management and Sharing Policy describes the expectations for data sharing for NIH-funded research. If the funder requires data sharing, accept the comment and provide the data. If the funder does not require data sharing, explain the policy to the reviewer.

How do I respond to a reviewer who asks me to add a coauthor?

The Committee on Publication Ethics Core Practices describe the criteria for authorship. If the reviewer asks you to add a coauthor who does not meet the authorship criteria, disagree with the comment and explain the authorship criteria. If the reviewer asks you to add a coauthor who meets the criteria, accept the comment and add the coauthor.

How do I respond to a reviewer who asks me to change the title?

Assess whether the reviewer's suggested title is more accurate or more informative. If the reviewer's title is better, accept the comment and change the title. If the reviewer's title is not better, disagree and explain why your original title is appropriate.

Using the Evidence

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References and Further Reading

• Research Methods Resources. National Library of Medicine.
• EQUATOR Network. EQUATOR Network.
• Core Practices. Committee on Publication Ethics.
• NIH Grants and Funding. National Institutes of Health.
• ORCID for Researchers. ORCID.
• Data Management and Sharing Policy. National Institutes of Health.
• NCBI Literature Resources. National Center for Biotechnology Information.
• PubMed. National Library of Medicine.

This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.