A protocol to prospectively study characteristics of meta-analyses submitted to a weekly medical journal raised several ethical issues. In submitting a manuscript for publication, authors do not implicitly consent to have their work used for research. Authors must be free to refuse to consent, without it affecting their chances for publication. Systematically analyzing data on manuscript characteristics might influence the decision to publish. Having investigators who are not on the editorial staff or peer reviewers extract the manuscripts' characteristics breaks the confidentiality of the author-editor-reviewer relationship. In response to these issues, we added a statement to our journal's instructions for authors that submitted manuscripts may be systematically analyzed to improve the quality of the editorial or peer review process. Authors had to actively consent to participate, but editors and external reviewers were unaware of which authors were participating. The manuscript characteristics were not shared with authors, editors, or external reviewers. The investigators were blinded to each manuscript's author and institution. After we addressed ethical issues encountered in studying manuscripts submitted to a medical journal, 99 of 105 authors submitting a meta-analysis during the study's first 24 months agreed to participate.