An editor deciding a borderline paper will often read the response letter before the revised manuscript, because it reveals whether the author understood the criticism.
Two failure modes dominate. Total capitulation, where every suggestion is implemented including the contradictory ones, producing an incoherent paper. And defensiveness, where the letter argues that the reviewers misread everything. Both are rejected.
Structure it so the editor can verify it
Reproduce each comment in full, in order, and answer directly beneath it. Do not summarise. Do not group thematically. The editor is checking that nothing was skipped, and anything that makes checking harder invites suspicion.
Each response needs three things:
- What you did, or did not do, in one sentence.
- Why, if that is not obvious.
- Where the change is, by section and page or line number.
The third is most often omitted and most wanted. “This has been clarified” forces the editor to hunt. “Clarified in Methods, paragraph two, page 7” can be verified in seconds.
Disagree properly
You may disagree. You may not dismiss. The difference is whether you engage with the reason behind the comment.
Poor: We do not agree that a larger sample was necessary.
Workable: We agree a larger sample would strengthen the estimate. Recruitment was capped by the ethics approval, which we now state in Limitations. The power calculation in Methods shows the achieved sample was adequate to detect the effect size specified in the protocol, and we have added that calculation.
The second concedes what is true, explains the constraint, and points to evidence.
Handle contradictory reviewers explicitly
When one wants the discussion expanded and another wants it cut, say so rather than quietly following one:
Reviewer 1 asked for the discussion to be expanded; Reviewer 2 asked for it to be shortened. We have removed the speculative passage on mechanism that Reviewer 2 identified, while adding the comparison with Ahmed et al. that Reviewer 1 requested.
This is the editor's problem, and naming it hands it back with a proposed solution.
Tone
Thank the reviewers once, briefly, at the top. Never speculate about a reviewer's motives or competence, even when a comment is plainly wrong — your letter is the only evidence of your professionalism the editor has.
What to submit
- The response letter as a separate file
- A clean copy of the revised manuscript
- A tracked-changes copy, unless the journal says otherwise
- Any new supplementary material referenced in your responses
If the decision was reject and resubmit, treat it as a revision. The same editor usually handles it, and addressing the original criticisms directly is what distinguishes a genuine resubmission. See also why papers are rejected.