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BackgroundSelective reporting of outcomes in clinical trials is a serious problem. We aimed to investigate the influence of the peer review process within biomedical journals on reporting of primary outcome(s) and statistical analyses within reports of randomised trials. MethodsEach month, PubMed (May 2014 to April 2015) was searched to identify primary reports of randomised trials published in six high-impact general and 12 high-impact specialty journals. The corresponding author of each trial was invited to complete an online survey asking authors about changes made to their manuscript as part of the peer review process. Our main outcomes were to assess: (1) the nature and extent of changes as part of the peer review process, in relation to reporting of the primary outcome(s) and/or primary statistical analysis; (2) how often authors followed these requests; and (3) whether this was related to specific journal or trial characteristics. ResultsOf 893 corresponding authors who were invited to take part in the online survey 258 (29%) responded. The majority of trials were multicentre (n = 191; 74%); median sample size 325 (IQR 138 to 1010). The primary outcome was clearly defined in 92% (n = 238), of which the direction of treatment effect was statistically significant in 49%. The majority responded (1–10 Likert scale) they were satisfied with the overall handling (mean 8.6, SD 1.5) and quality of peer review (mean 8.5, SD 1.5) of their manuscript. Only 3% (n = 8) said that the editor or peer reviewers had asked them to change or clarify the trial’s primary outcome. However, 27% (n = 69) reported they were asked to change or clarify the statistical analysis of the primary outcome; most had fulfilled the request, the main motivation being to improve the statistical methods (n = 38; 55%) or avoid rejection (n = 30; 44%). Overall, there was little association between authors being asked to make this change and the type of journal, intervention, significance of the primary outcome, or funding source. Thirty-six percent (n = 94) of authors had been asked to include additional analyses that had not been included in the original manuscript; in 77% (n = 72) these were not pre-specified in the protocol. Twenty-three percent (n = 60) had been asked to modify their overall conclusion, usually (n = 53; 88%) to provide a more cautious conclusion. ConclusionOverall, most changes, as a result of the peer review process, resulted in improvements to the published manuscript; there was little evidence of a negative impact in terms of post hoc changes of the primary outcome. However, some suggested changes might be considered inappropriate, such as unplanned additional analyses, and should be discouraged.