Nowadays, scientometrics has become an important field of study to monitor the progresses in scientific performance of a research group, a department, a university etc. A number of scientometrical studies have been done about Iranian scientific outcome in recent years. But there is no comparison between major Iranian medical universities. In this study, by using Scopus as search engine, the scientific outcomes have been compared with each other. These universities were compared by the number of published articles per year, number of citations received per year, number of citations received per year per article, total H-indices, top ten authors, and top ten journals. The results of this study show that the order of the studied universities in research performance is as follow: Tehran [ Shiraz = Shahid Beheshti [ Isfahan = Iran [ Tabriz = Mashhad universities of medical sciences. In addition, the data of Tehran University of Medical Sciences as the top medical university of Iran was compared with some of top medical universities around the world.