This report describes the steps in the development of an accreditation system for medical universities in the Islamic Republic of Iran. The national accreditation project, supported by the government, was performed from 2001 to 2005. The project was carried out in 3 main phases, each phase including a number of tasks. After a review of the international literature on accreditation and through national consensus, a set of national institutional accreditation standards was developed, including 95 standards and 504 indicators in 10 areas. By complying with accepted national standards, Iranian medical universities will play an important role in promoting health system performance.