Numbering Reviewer Comments: A Simple System to Eliminate Confusion
By Dr. Zubair Khalid, DVM, MS, PhD ·
Quick Answer
- Number every reviewer comment with a code that includes the reviewer number and the comment number, such as R1-1 or R2-3, so each response maps to exactly one comment.
- Build your response letter as a table with columns for comment code, full comment text, your response, and the location of the change in your revised manuscript.
- Keep the same comment codes in your response letter, your tracked-changes manuscript, and your cover letter so reviewers never have to search for a match.
At a Glance
| Comment Code | Meaning | Example Use |
|---|---|---|
| R1-1 | Reviewer 1, first comment | R1-1 appears above the response to the first comment from Reviewer 1 |
| R2-3 | Reviewer 2, third comment | R2-3 appears above the response to the third comment from Reviewer 2 |
| R3-7 | Reviewer 3, seventh comment | R3-7 appears above the response to the seventh comment from Reviewer 3 |
Why Comment Numbering Fails in Practice
Researchers often receive multiple reviewer reports with comments that are not numbered by the journal. When you copy comments into a response letter without a consistent code, reviewers cannot tell which response belongs to which comment. This confusion leads to repeated email exchanges, delayed decisions, and sometimes a request for another revision round.
The most common failure is using vague labels such as "Comment 1" for every reviewer. If Reviewer 1 and Reviewer 2 both have a "Comment 1," the reviewer cannot know whether your response addresses their comment or the other reviewer's comment. Another failure is reordering comments to group them by topic. When you reorder, the reviewer must hunt through your letter to find their original comment, and they may conclude that you ignored it.
A third failure is numbering comments only in your response letter but not in your revised manuscript. Reviewers often want to verify that you made the change they requested. If your manuscript does not show where each change occurred, the reviewer must compare the entire manuscript against your letter, which is time-consuming and error prone.
The Core Principle of Comment Coding
The core principle is that every comment receives a unique code that never changes throughout the revision process. The code has two parts. The first part identifies the reviewer, and the second part identifies the comment within that reviewer's report.
Use the letter R followed by the reviewer number, then a hyphen, then the comment number. For example, R1-1 is the first comment from Reviewer 1, and R2-3 is the third comment from Reviewer 2. This system works for any number of reviewers and any number of comments per reviewer.
The code must be stable. If you decide to merge two comments into one response, assign a new code such as R1-4a and R1-4b instead of renumbering everything. If you decide to split one comment into two responses, use R1-5a and R1-5b. Renumbering creates confusion because the reviewer may have already started reading your letter with the original numbering in mind.
How to Build Your Response Letter
Start by creating a table with four columns. The first column holds the comment code. The second column holds the full text of the reviewer's comment, copied exactly as the reviewer wrote it. The third column holds your response. The fourth column holds the location of the change in your revised manuscript, such as "Methods, paragraph 2" or "Figure 3 legend."
Copy the reviewer's comment exactly. Do not paraphrase or shorten it. The reviewer needs to see their own words to confirm that you understood the comment. If the comment is long, keep it in full. If the comment contains multiple subpoints, keep them together under one code and address each subpoint in your response.
Write your response in plain language. State what you did, why you did it, and where the change appears. If you disagree with the comment, explain your reasoning with evidence from your study or from published literature. Do not use defensive language. A respectful response that explains your reasoning is more likely to be accepted than a response that simply says "We disagree."
In the location column, be specific. Instead of writing "Results," write "Results, paragraph 3, sentence 2." Instead of writing "Figure 2," write "Figure 2, panel B, legend." The more specific you are, the easier it is for the reviewer to verify your change.
How to Handle Multiple Reviewers
When you receive reports from two or more reviewers, create a separate section in your response letter for each reviewer. Use an H3 heading such as "Responses to Reviewer 1" and "Responses to Reviewer 2." Within each section, list the comments in the same order the reviewer wrote them.
Do not combine comments from different reviewers into one table. Each reviewer should see their own comments and responses without having to filter out another reviewer's content. This separation also helps the editor, who may send your response letter to each reviewer separately.
If two reviewers made the same comment, respond to each reviewer separately. Do not write "See response to Reviewer 1" in your response to Reviewer 2. The second reviewer may not see the first reviewer's report, and even if they do, they expect a direct response to their own comment.
How to Handle Major and Minor Comments
Journals sometimes separate comments into "Major Comments" and "Minor Comments." Keep this distinction in your response letter. Use a subheading for each category, and number the comments within each category separately. For example, under "Major Comments," use R1-M1, R1-M2, and so on. Under "Minor Comments," use R1-m1, R1-m2, and so on.
This approach preserves the reviewer's own organization while still giving every comment a unique code. If the reviewer did not separate major and minor comments, do not create the distinction yourself. Use the simple R1-1, R1-2 numbering instead.
How to Reference Changes in Your Manuscript
Your response letter should tell the reviewer exactly where to find each change. Use the location column in your table for this purpose. In your revised manuscript, mark each change so the reviewer can spot it quickly.
Most journals ask you to submit a tracked-changes version and a clean version. In the tracked-changes version, use the comment code in the margin or in a comment bubble next to the change. For example, write "R1-1" in the margin next to the sentence you revised in response to that comment. This direct link between the manuscript and the response letter saves the reviewer time and reduces the chance of a misunderstanding.
If your journal does not support comment bubbles, add the code in brackets at the end of the revised sentence, such as "[R1-1]." Remove these brackets before submitting the final version if the journal requires a clean manuscript.
Common Failure Patterns and How to Avoid Them
| Failure Pattern | Consequence | Prevention |
|---|---|---|
| Using "Comment 1" for every reviewer | Reviewer cannot tell which response is theirs | Use R1-1, R2-1, R3-1 codes |
| Reordering comments by topic | Reviewer cannot find their original comment | Keep the reviewer's original order |
| Renumbering after merging or splitting | Reviewer loses track of the response | Use subcodes such as R1-4a and R1-4b |
| No location column | Reviewer must search the whole manuscript | Add a specific location for every change |
| Paraphrasing the reviewer's comment | Reviewer doubts you understood the comment | Copy the comment exactly |
Practical Steps for Assembling Your Response Letter
Follow these steps in order. Each step builds on the previous one, and skipping a step creates extra work later.
- Read all reviewer reports and the editor's decision letter. Identify how many reviewers provided comments and whether the editor added their own comments.
- Create a new document for your response letter. Use the journal name and manuscript number in the title.
- Copy each reviewer's comments into the document in the original order. Assign a code to each comment as you copy it.
- Build the table for each reviewer with the four columns described above.
- Write your response to each comment. Address every part of the comment, including subpoints.
- Revise your manuscript. As you make each change, note the location in your response letter.
- Add the comment code to the tracked-changes version of your manuscript next to each change.
- Read the entire response letter from the perspective of a reviewer. Check that every comment has a response and every response has a location.
- Submit the response letter, the tracked-changes manuscript, and the clean manuscript according to the journal's instructions.
Records and Measurements to Keep
Keep a revision log that tracks each comment code, the date you addressed it, and the location of the change. This log helps you monitor your progress and provides a record if you need to escalate a dispute.
Your revision log should include the following columns: comment code, reviewer number, comment summary, date addressed, location of change, and status. Update the log after each working session. This practice prevents you from discovering at the submission deadline that you forgot to address a comment.
The log also helps you measure how much work remains. If you have 20 comments and you have addressed 15, you know that five remain. This measurement is useful when you are planning your revision timeline.
How to Respond When You Disagree With a Comment
You are allowed to disagree with a reviewer's comment. The key is to disagree respectfully and with evidence. State that you appreciate the reviewer's concern, explain why you believe your original approach was appropriate, and provide supporting evidence from your data or from published literature.
If you decide not to make a change, say so clearly. Do not write a vague response that implies you made a change when you did not. Reviewers detect this quickly, and it damages your credibility.
If the reviewer asked you to add an analysis that you believe is not feasible, explain the limitation. State what you tried, what happened, and why the analysis cannot be done with your current data. If the analysis is possible but would take more time than the revision period allows, say so and offer an alternative.
Professional Escalation Criteria
Most revision processes proceed without conflict. However, you may encounter situations that require escalation to the editor. Escalate when a reviewer makes demands that are impossible to meet, when a reviewer is abusive or unprofessional, or when you believe the review process has been unfair.
Contact the editor directly and explain the situation. Provide the comment code and the full text of the problematic comment. State what you have done to address the comment and why you believe the demand is unreasonable. The editor has the authority to mediate disputes between authors and reviewers.
Do not escalate for minor disagreements. The revision process is designed to improve your manuscript, and most reviewer comments, even when they seem harsh, contain useful feedback. Reserve escalation for cases where the process itself has broken down.
Welfare and Safety Context for Animal Research
If your manuscript involves animal research, your response letter must address reviewer comments about animal welfare and experimental rigor. Reviewers may ask about housing conditions, sample sizes, anesthesia protocols, or humane endpoints. Respond to these comments with the same comment-code system you use for other comments.
Your responses should reference the ethical approval you obtained from your institutional animal care and use committee. If the reviewer asks for details that are not in your manuscript, add them to the methods section and cite the location in your response letter. The National Library of Medicine provides access to biomedical research references that can support your responses about animal research methods.
Reporting Guidelines and Transparent Research
Reviewers often ask authors to follow reporting guidelines for their study type. The EQUATOR Network maintains a library of reporting guidelines for different study designs. If a reviewer asks you to follow a specific guideline, locate the guideline on the EQUATOR Network, read the checklist, and revise your manuscript accordingly.
In your response letter, state which guideline you followed and where the checklist items appear in your manuscript. Use the comment-code system to link each checklist item to the relevant reviewer comment. This approach shows the reviewer that you take reporting standards seriously.
Publication Ethics and Peer Review
The Committee on Publication Ethics describes core practices for peer review, authorship, and publication. These practices apply to your revision process. For example, you must not add an author to the revised manuscript without the editor's permission and the new author's consent. You must not fabricate data to address a reviewer's comment.
If a reviewer asks you to include data that you do not have, do not invent it. Explain that the data are not available and describe what you can do instead. The editor will understand that you cannot create data that do not exist.
Funding and Grant Context
If your research was funded by a grant, your revision process may affect your grant reporting. The National Institutes of Health provides guidance on grant policy and award management. If your revision requires additional experiments that extend beyond your funded scope, you may need to discuss this with your program officer.
Your response letter does not need to mention funding unless the journal requires a funding statement. However, you should be aware that major revisions can delay publication, which may affect your grant timeline. Plan your revision schedule with your funding obligations in mind.
Data Management and Sharing
The NIH Data Management and Sharing Policy describes expectations for data management and sharing in NIH-funded research. Reviewers may ask you to share your data or to describe your data-sharing plan. Respond to these comments with the same comment-code system.
If your manuscript includes a data availability statement, update it to reflect any changes you made during revision. If the reviewer asks for access to your data, provide it through the repository you named in your data-sharing plan. Do not share data that would compromise participant privacy or that you are not authorized to share.
Researcher Identity and ORCID
Your response letter should include your ORCID identifier if the journal requires it. The ORCID for Researchers page explains how to maintain your researcher record. During the revision process, update your ORCID record if your affiliation or funding information has changed.
Reviewers do not typically comment on ORCID identifiers. However, the journal may ask you to confirm your ORCID during submission. Keep your ORCID record current so that your published manuscript links correctly to your other work.
Limitations of the Comment-Numbering System
The comment-numbering system works well for most revisions, but it has limitations. If a reviewer writes a long narrative comment that covers multiple distinct issues, a single code may not capture the complexity. In this case, split the comment into subcodes such as R1-2a and R1-2b, and respond to each subpoint separately.
The system also assumes that the reviewer's comments are stable. If the editor sends you additional comments after the initial decision, assign new codes to those comments and add them to your response letter. Do not renumber the existing comments.
Finally, the system does not solve the problem of a reviewer who does not read your response letter carefully. You can make your letter as clear as possible, but you cannot control how the reviewer reads it. The best you can do is make the letter easy to navigate and verify.
How to Check Your Work Before Submission
Before you submit your response letter, read it from the perspective of a reviewer who has never seen it. Ask yourself the following questions. Can I find my comment quickly? Can I see the response to my comment without reading other responses? Can I find the change in the manuscript without searching the entire document?
If you answer no to any of these questions, revise your letter. Add more specific locations. Break up long responses. Move the comment text closer to the response. The goal is to make the reviewer's job as easy as possible.
Ask a colleague to read your response letter and check that every comment has a response and every response has a location. A fresh pair of eyes often catches problems that you have become blind to after working on the revision for days.
Decision Framework for Choosing a Comment Numbering Scheme
The R1-1 system works well for most revisions, but it is not the only viable scheme. Your choice of numbering format should depend on the journal's submission system, the structure of the reviewer reports, and the complexity of your revision. This section presents a practical decision framework to help you select the right scheme before you begin building your response letter.
Step 1: Assess the Journal Submission System
Start by checking how the journal's online submission portal handles reviewer comments. Some portals automatically assign numbers to reviewer comments when they generate the decision letter. If the portal already provides numbers, use those numbers exactly as they appear. Do not create your own numbering that conflicts with the portal's numbering, because the reviewer may refer to the portal's numbers in their own notes.
If the portal does not number comments, check whether it allows you to upload a response letter as a separate file or whether it requires you to enter responses into text fields. Some systems display each reviewer comment in a box with a response field directly beneath it. In that case, you may not need codes at all, because the system already links each response to its comment. However, you should still include codes in your uploaded manuscript so the reviewer can find the location of each change.
Step 2: Match the Scheme to the Reviewer Report Structure
Examine how the reviewer organized their comments. Three common structures appear in practice.
Structure A: Numbered list. The reviewer wrote "1." "2." "3." or used bullet points. Use the reviewer's own numbers as the second part of your code. If the reviewer numbered comments 1 through 12, your codes are R1-1 through R1-12. This preserves the reviewer's mental model and makes it easy for them to find their comment.
Structure B: Unnumbered paragraphs. The reviewer wrote continuous paragraphs without numbers or bullets. Assign your own sequential numbers in the order the paragraphs appear. Your codes become R1-1, R1-2, R1-3, and so on. Copy each paragraph in full so the reviewer can match your code to their text.
Structure C: Themed sections. The reviewer grouped comments under headings such as "Major Issues" and "Minor Issues" or "Statistical Concerns" and "Clarity Issues." Preserve these groupings in your response letter. Use subcodes that reflect the grouping, such as R1-M1 for the first major comment and R1-m1 for the first minor comment. This approach keeps the reviewer's organization intact while still giving every comment a unique code.
Step 3: Decide Whether to Use Subcodes
Subcodes become necessary when a single comment contains multiple distinct requests that require separate responses. Use the decision rule that a comment needs subcodes when you cannot answer it with one coherent response paragraph. For example, if a reviewer writes "Please clarify your inclusion criteria and also report the confidence intervals for your primary outcome," you have two distinct requests. Respond to each separately using R1-4a for the inclusion criteria and R1-4b for the confidence intervals.
Do not create subcodes for comments that are already short and focused. Adding subcodes to every comment creates unnecessary complexity. Reserve subcodes for comments that genuinely contain multiple independent requests.
Step 4: Apply the Consistency Test
Before you commit to a numbering scheme, run a consistency test. Write out the first three codes you plan to use and check that they meet these criteria. The code identifies the reviewer without ambiguity. The code preserves the reviewer's original order. The code remains stable even if you merge or split comments later. The code appears identically in your response letter, your tracked-changes manuscript, and your cover letter.
If any of these criteria fail, adjust your scheme before you start writing responses. Changing codes after you have written responses creates rework and increases the chance of a mismatch.
Comparison of Numbering Schemes
| Scheme | Best Used When | Example | Limitation |
|---|---|---|---|
| R1-1, R1-2 | Reviewer comments are unnumbered paragraphs | R1-1 for first comment from Reviewer 1 | Requires you to assign numbers yourself |
| R1-M1, R1-m1 | Reviewer separated major and minor comments | R1-M1 for first major comment | More complex codes to track |
| Portal-assigned numbers | Journal system already numbers comments | Use the exact numbers from the portal | You cannot control the format |
| E1, E2 for editor | Editor added separate comments | E1 for first editor comment | Only works when editor comments exist |
| R1-4a, R1-4b | One comment contains multiple distinct requests | R1-4a for first subpoint of comment 4 | Adds complexity to the code |
Step 5: Document Your Scheme Before Writing Responses
Write your chosen scheme at the top of your response letter document. Include an example such as "R1-1 refers to the first comment from Reviewer 1" so that anyone who opens the document understands the system immediately. This documentation is especially important if you collaborate with coauthors who will help write responses.
Record the scheme in your revision log as well. Add a column for the numbering scheme you selected and note any subcodes you create during the revision process. This record prevents two coauthors from assigning different codes to the same comment.
Troubleshooting Common Scheme Selection Problems
Problem: The journal portal numbers comments differently from the reviewer's own numbering. Some reviewers number their comments in their report, but the journal portal assigns different numbers when it ingests the report. Use the portal's numbers in your response letter because that is what the editor and reviewer see in the submission system. Add a note in your response letter that says "Comment numbers refer to the numbers assigned by the submission system."
Problem: You receive supplementary comments from the editor after you have already built your response letter. Assign new codes to the editor's comments using E1, E2, and so on. Add them as a separate section at the end of your response letter. Do not renumber your existing reviewer codes.
Problem: A reviewer comment is so long that it spans multiple pages. Keep the entire comment under one code. Do not split it into multiple codes unless the comment contains clearly distinct requests. If you must split it, use subcodes and explain in your response that you divided the comment to address each part separately.
Problem: Two reviewers make identical comments. Respond to each reviewer separately with their own code. Do not write "See response to Reviewer 1" because the second reviewer may not have access to the first reviewer's report. Duplicate responses are acceptable and expected in this situation.
When to Reconsider Your Scheme
If you find yourself writing explanations about your numbering system in your response letter, your scheme is too complicated. A good scheme requires no explanation beyond a single line at the top of the document. If you need to write paragraphs explaining how your codes work, simplify the scheme.
If you catch yourself renumbering comments after you have started writing responses, stop and reassess. Renumbering is the most common source of errors in response letters. The stability of your codes matters more than the elegance of the scheme. A simple scheme that you follow consistently outperforms a complex scheme that you keep changing.
Frequently Asked Questions
Should I number comments separately for each reviewer?
Yes. Use R1 for Reviewer 1, R2 for Reviewer 2, and R3 for Reviewer 3. Number the comments within each reviewer's report separately, such as R1-1, R1-2, R2-1, R2-2. This system prevents confusion when multiple reviewers make similar comments.
What do I do if a reviewer comment has multiple parts?
Keep the comment under one code and address each part in your response. If the parts are distinct enough that you need separate responses, split the code into subcodes such as R1-3a and R1-3b. Do not renumber the other comments.
How do I reference a change in my revised manuscript?
Use the location column in your response table. Write the specific location, such as "Methods, paragraph 2, sentence 3" or "Figure 2, panel B." In your tracked-changes manuscript, add the comment code next to the change so the reviewer can find it quickly.
What if I disagree with a reviewer's comment?
State your disagreement respectfully and provide evidence. Explain why you believe your original approach was appropriate. If you decide not to make a change, say so clearly. Do not imply that you made a change when you did not.
Can I reorder comments to group them by topic?
No. Keep the reviewer's original order. Reordering makes it hard for the reviewer to find their comments and may lead them to think you ignored a comment. If you want to group related comments, do so in your response text while keeping the original order.
What should I do if the editor adds their own comments?
Treat the editor's comments as a separate section in your response letter. Use codes such as E1, E2, and E3 for the editor's comments. Respond to them with the same level of detail as you respond to reviewer comments.
How long should my response letter be?
Your response letter should be as long as it needs to be to address every comment. There is no standard length. A thorough response letter that addresses every comment is better than a short letter that leaves questions unanswered.
What if I cannot complete a requested analysis?
Explain the limitation in your response. State what you tried, what happened, and why the analysis cannot be done with your current data. If the analysis is possible but would take more time, say so and offer an alternative. Do not fabricate data to satisfy the reviewer.
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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.