Background: The number of scientific publication by a country is an important indication of its science generation and development. The aim of this study was to compare the publications in medical sciences of Islamic countries from 2002-2009 with those of a number of developed countries. Methods: The PubMed and CIA World Fact Book were used to extract the number of publications and socioeconomic status of target countries, respectively. The number of publications, publications per million population, gross domestic product (GDP) per capita, population below poverty line (PBP) and type of publications of the countries were compared. Results: The publications of Islamic countries increased from 6906 in 2002 to 21656 in 2009. There was a positive correlation between GDP per capita and publication per million. However, publication productivity did not decrease significantly with the increase of PBP. Turkey and Iran were top two among Islamic countries in terms of the number of publications and growth of the rate of scientific publication, respectively. Islamic countries do lag behind developed countries in terms of the number of publication and the rate of growth. Conclusion: There is a wide gap between developed and Islamic countries and among Islamic countries themselves in terms of the number and the rate of growth of publication in medical sciences.