Introduction: Scientific output of the Islamic Republic of Iran in Medical Sciences has been increased during recent years as reflected in Scopus database. Moreover, highly cited papers of researchers, institutions and countries can be used in order to study the citation impact and quality of scientific output. The current study investigates the quality of Medical Sciences’ scholarly output of Iran through analysis of its progress in publishing highly cited papers compared to the top 25 most productive countries in the world. 

Methods: To conduct this study, scientometric indicators were utilized. A total of 45065 papers published by Iranian Medical Science researchers during 2010-2014 and indexed in the Scopus were selected as the sample of the study. The contribution of Iranian researchers and institutions in top 1%, 10% and 25% highly cited papers in the world was studied.

Results: Results of the study revealed that 0.35% of the country’s total output in Medical Sciences was among the top 1% most highly cited papers in the world during the time period of this study. This share is 4.9% and 17.39% based on top 10% and 25% citation threshold, respectively. Iran ranked 25^th in top 1% as well as 24^th in top 10% and 25% by share of highly cited papers, among most 25 productive countries in the world. Although the proportion of highly cited papers in the country’s total output was found to be relatively small compare to other leading countries, but Iran showed the highest growth rate in publication of highly cited papers over 5-year time span

Conclusion: Beside the quantity Iran’s scholarly publication in Medical Sciences fields, the quality of these output show the increasing trend based on the share of highly cited papers.