Two reviewers rarely read a manuscript the same way, and it is routine for their comments to point in opposite directions: one asks you to remove an exploratory analysis, the other asks you to expand it; one wants a claim strengthened, the other wants it hedged. This guide is a decision framework for that specific situation — how to diagnose whether a contradiction is real, decide which request to follow when you cannot satisfy both, and document the resolution so the editor can see your reasoning was principled rather than arbitrary.
This is a narrower, deeper treatment of one problem than CASRAI’s guide on how to write a response to reviewers letter, which covers the letter’s overall structure, tone, and formatting and touches conflicting requests only briefly. If you haven’t yet drafted the letter itself, start there for the mechanics; come here specifically for how to resolve a genuine contradiction between reviewers before you write the paragraph that explains it. See also CASRAI’s guide to what a revise and resubmit decision actually means if you’re earlier in the process.
What counts as a genuine contradiction
Not every pair of divergent comments is a true conflict. Before treating something as a contradiction to resolve, check which of these it actually is:
- A true contradiction. Satisfying one request necessarily undoes the other — Reviewer 1 asks you to delete the subgroup analysis in Section 3.2, Reviewer 2 asks you to expand it with additional covariates. You cannot do both to the same passage.
- Independent points that look related. Reviewer 1 wants clearer methods reporting; Reviewer 2 wants a different statistical test. These can usually both be satisfied without one undermining the other — don’t manufacture a conflict where there’s just two separate revisions to make.
- Different emphasis, not opposite instructions. One reviewer stresses brevity generally, another stresses completeness generally, without either pointing at the same specific passage. This is a tension to manage across the whole revision (see word-count guidance below), not a single contradiction to adjudicate.
- One reviewer is factually mistaken. Occasionally what looks like a conflict is really one reviewer’s comment resting on a misreading of the current text or the literature. If a careful re-check shows this, the correct response is a courteous, evidence-based correction to that reviewer via the response letter and editor — not a negotiated compromise with a request that has no technical basis.
Only the first category — a true contradiction, where the manuscript cannot simultaneously satisfy both instructions — needs the resolution process below.
A framework for resolving a genuine contradiction
1. Identify what each reviewer is actually optimizing for
Reviewers rarely explain their underlying priority, but it’s usually inferable from the rest of their report. A request to shorten a section is often really about readability or proportionality to the paper’s contribution; a request to expand the same section is often about methodological transparency or robustness. Naming the underlying concern, not just the surface instruction, is what makes a synthesis possible in the next step.
2. Look for a synthesis before picking a side
Many apparent either/or conflicts have a third option that addresses both underlying concerns even though it satisfies neither literal instruction exactly:
- Move detail to a supplementary appendix or online-only material — satisfies the reviewer who wants transparency without lengthening the main text for the reviewer who wants brevity.
- Summarize the disputed content in the main text with a pointer to full detail elsewhere (methods appendix, repository, protocol registration).
- Restructure rather than delete or expand — if the concern is that a subsection is out of proportion to its importance, moving it (not cutting or growing it) can resolve both objections.
A synthesis is the strongest outcome because it lets your response letter say, honestly, that both reviewers’ underlying concerns were addressed — not that one was chosen over the other.
3. When no synthesis exists, decide on merit and journal fit
Sometimes the requests are genuinely incompatible and a synthesis isn’t available — you have to choose. Weigh, in this order:
- Scientific validity first. If one request would introduce a methodological problem (e.g., removing a caveat that a result is preliminary, or omitting a limitation that materially affects interpretation), validity outweighs either reviewer’s stylistic preference.
- Journal scope and audience. A request that better matches the journal’s stated scope, word-limit policy, or house style carries more weight than one that doesn’t — a reviewer’s personal preference for more mathematical detail, for instance, may not fit a journal aimed at a clinical readership.
- Reviewer expertise relative to the specific point. If your journal’s submission system discloses reviewer expertise areas, or it’s evident from their comments which reviewer is closer to the specific sub-question in dispute (e.g., a biostatistics-focused reviewer’s comment on an analytic method versus a clinically-focused reviewer’s comment on the same passage), that’s a legitimate factor — but state your reasoning rather than silently deferring to perceived seniority or expertise.
- Preserve the more conservative option when validity is genuinely ambiguous. Between two plausible resolutions with no clear scientific edge, the option that adds a limitation, caveat, or clarifying detail rather than removes one is usually the safer default with an editor and future readers.
4. Document the resolution transparently, addressed to both reviewers
The response letter is where the reasoning becomes visible to the editor, who is the one person able to see both reviewer reports side by side. Name the conflict explicitly rather than quietly picking a side and hoping neither reviewer notices at a second round:
“Reviewer 1 requested that the exploratory subgroup analysis (original Section 3.2) be removed as underpowered; Reviewer 2 requested it be expanded with additional covariates. We have retained the analysis but moved it to a new Supplementary Appendix B, reframed as exploratory and hypothesis-generating rather than confirmatory, and added the requested covariates there. The main text now summarizes the finding in two sentences (Results, p. 9) with a pointer to the full appendix, which we believe addresses Reviewer 1’s proportionality concern and Reviewer 2’s request for methodological depth without asking either reviewer to fully concede their original point.”
This example is an illustrative composite constructed to demonstrate the structure of a resolution paragraph, not a real exchange from a specific manuscript or journal. Three things this paragraph does that a shorter “we have addressed both reviewers’ comments” would not: it names both reviewers and quotes their positions in miniature so each can verify their concern was actually read; it states the resolution as a concrete, checkable change rather than an assurance; and it explains the logic connecting the change to both underlying concerns, which is what signals a principled decision rather than an arbitrary one.
5. Escalate genuine impasses to the editor, not to the reviewers directly
Occasionally there is no defensible synthesis and no clear scientific basis for preferring one reviewer’s position — both requests are reasonable and mutually exclusive. In that situation, it is appropriate and expected to say so plainly in the cover letter or a clearly labeled note to the editor, rather than silently choosing and hoping it doesn’t resurface. Editors, not reviewers, hold the authority to weigh reviewer input against each other and make a binding call — that is a normal, expected part of an editor’s role in the process (see CASRAI’s guide on editorial board responsibilities). Framing this for the editor works best when it stays neutral and specific: state both positions, state what you did in the interim (usually the more conservative or synthesis option, even if partial), and ask directly for the editor’s guidance on which to prioritize if your interim choice isn’t acceptable.
Common mistakes to avoid
- Silently picking a side. Implementing one reviewer’s request and ignoring the other’s without any acknowledgment reads, at a second round of review, as though the comment was missed or dismissed — even if your underlying reasoning was sound.
- Arguing with a reviewer’s competence in the response letter. Even where one reviewer is genuinely mistaken on a factual point, the corrective response should address the specific claim with evidence, not characterize the reviewer as wrong in general terms.
- Treating every disagreement as requiring editor escalation. Routing every minor tension to the editor when a synthesis was available reads as either indecisive or as offloading a decision the author was well placed to make — reserve escalation for genuine, unresolvable impasses.
- Letting the conflict stall the revision. A resolution that is reasonable and clearly explained, even if imperfect, moves the process forward; waiting for certainty before responding usually just delays a second round of review where the same tension resurfaces anyway.
- Resolving the conflict only in the manuscript, not in the response letter. A change that quietly favors one reviewer without an explanatory note leaves the disadvantaged reviewer to notice the omission themselves at the next round, which reads worse than an upfront explanation would have.
A note on single-reviewer self-contradiction
A related but distinct situation is a single reviewer whose own comments pull in different directions across their report — for example, asking early on for a more concise introduction and later asking for additional background context that would lengthen it. The same diagnostic questions apply (is this a true contradiction or just competing priorities across the whole report), but because there’s only one reviewer to reconcile with, the response letter can address it directly and briefly to that reviewer rather than needing the cross-reviewer framing above: acknowledge both comments, explain the balance struck, and point to where in the revised manuscript that balance is visible.
Where this fits with other CASRAI guides on peer review response
This guide assumes you already understand the basic structure of a response letter. For the point-by-point format, tone, and a worked example of a complete letter, see how to write a response to reviewers letter. For how response letters differ by the scale of revision requested and by publisher, see peer review response letters: major vs. minor revisions across publisher templates. If a conflict is severe enough to be about scope reduction driven by a journal’s length limits rather than reviewer disagreement, see manuscript word count limits and how to shorten a submission. To see what reviewer comments actually look like in practice, including cases that led to rejection, see reviewer comments on a rejected manuscript: a worked example and reviewer report: a complete worked example. If the disagreement follows an outright rejection rather than a revise-and-resubmit invitation, the relevant document is different — see how to write an appeal letter to a journal editor.
Frequently asked questions
What if I genuinely cannot satisfy either reviewer without compromising the science?
State this directly to the editor rather than forcing a change you believe is scientifically unsound. Explain the technical basis for your position, note both reviewers’ requests, and propose what you believe is the scientifically defensible option — editors expect and routinely receive this kind of pushback when it’s evidence-based rather than a refusal to engage.
Should I tell Reviewer 1 what Reviewer 2 said?
Yes, within the response letter’s normal structure. Response letters go to the editor, who typically shares each author response with all reviewers at the next round, so naming the conflict (“Reviewer 1 requested X; Reviewer 2 requested the opposite”) is transparent and expected, not something that needs separate disclosure outside the letter.
Does the editor expect me to resolve every conflict myself?
No. Editors expect authors to make a reasonable, well-explained attempt at resolution, but genuine impasses are a normal part of the process and editors retain final authority over the decision. What editors do expect is that you engaged with both comments rather than silently ignoring one.
What if a third reviewer’s comments create a three-way conflict?
The same framework applies with a three-way version of step 1 (identify each reviewer’s underlying concern) and step 2 (look for a synthesis satisfying all three, or the largest subset possible). With three or more conflicting positions a synthesis is less likely, which makes editor escalation more common and more clearly appropriate at that point.
