Providing a perfect instruction to authors can prevent most potential publication ethics errors. This study was conducted to determine the quality of ethical considerations in the instructions to the authors of Iranian research scientific journals of medical sciences (accredited by the Commission for Accreditation and Improvement of Iranian Medical Journals) in October 2011. Checklist items (n=15) were extracted from the national manual of ethics in medical research publications, and the validity of the manual of ethics was assessed. All the accredited Iranian journals of medical sciences (n=198) were entered into the study. The instructions to the authors of 160 accredited Iranian journals were available online and were reviewed. The ANOVA and Kendall Correlation coefficient were performed to analyze the results. A total of 76 (47.5%) of the 160 journals were in English and 84 (52.5%) were in Farsi. The most frequently mentioned items related to publication ethics comprised “commitment not to send manuscripts to other journals and re-publish manuscripts” (85%, 83.8%), “aim and scope” of the journal (81.9%), “principles of medical ethics in the use of human samples” (74.4%), and “review process” (74.4%). On the other hand, the items of “principles of advertising” (1.2%), “authorship criteria” (15%), and “integrity in publication of clinical trial results” (30.6%) were the least frequently mentioned ones. Based on the study findings, the quality of publication ethics, as instructed to the authors, can improve the quality of the journals.