Objective During peer review, submitted manuscripts are scrutinised by independent experts to assist journal editors in their decision-making and to help improve the quality of articles. In this retrospective cohort study, peer review comments for drug trials submitted to medical journals were analysed to investigate whether there is a relation between the content of these comments and sponsorship, direction of results and decision about acceptance.

Design/setting Descriptive content analysis of reviewer comments made on manuscripts on drug trials submitted to eight medical journals (January 2010–April 2012). For each manuscript, the number of reviewers, decision about acceptance, sponsorship and direction of results were extracted. Reviewer comments were classified using a predefined checklist.

Results Reviewer reports for 246 manuscripts were assessed. Industry-sponsored trials were more likely to receive comments about lack of novelty (8.9%) than industry-supported (2.5%) and non-industry trials (6.1%, overall p=0.038). Non-industry trials more often received comments about poor experimental design (69.7%) than industry-supported (58.8%) and industry-sponsored trials (52.9%, overall p=0.019). Non-industry trials were also more likely to receive comments regarding inappropriate statistical analyses (28.4%) than industry-supported (23.5%) and industry-sponsored trials (15.1%, overall p=0.006). Manuscripts with negative results were more likely to receive comments about inappropriate conclusions (29.3%) than those with positive results (18.9%, p=0.010). Rejected manuscripts had more often received comments on the research question not being clinically relevant (7.8%) than accepted manuscripts (1.6%, p=0.002), and also on lack of novelty (8.3% vs 2.6%, p=0.008) and poor experimental design (68.6% vs 50.5%, p<0.001).

Conclusions Reviewers identified fewer shortcomings regarding design and statistical analyses in industry-related trials, but commented more often on a lack of novelty in industry-sponsored trials. Negative trial results did not significantly influence the nature of comments other than appropriateness of the conclusion. Manuscript acceptance was primarily related to the research question and methodological robustness of studies.