The national guidelines for biomedical research ethics are approved by the "National Committee for Ethics in Biomedical Research" at the Iranian Ministry of Health and Medical Education as the regulatory body for biomedical research in the country. The focus of these guidelines should be on the ethical issues related to different stages of the research process, which would lead to increased research integrity and better supervision of research activities. The present study analyzed the contents of these national guidelines to clarify the ethical considerations connected to the five stages of a research process including 1) proposing, 2) approval, 3) operation, 4) documentation and 5) publishing. The findings showed that the assessed guidelines laid more emphasis on the ethical considerations related to the research operation stage rather than the proposal stage. In other words, activities such as identification of the research problem, formulation of hypotheses and questions, financial evaluation, data analysis and data interpretation did not receive adequate attention in these guidelines. Most of the guidelines presented subject categories such as the rights of participants and supervisory considerations in the "research operation stage", ethical considerations in the "evaluation and approval procedure stage", and editorial responsibilities in the "research review and publication stage". In general, despite noticeable content for guiding researchers for ethical conduction of research the national guidelines are not adequately developed to cover comprehensive and sufficient ethical considerations regarding all the activities of research