Background: Measuring scientific outputs allows for objective evaluation of established health research systems and ranking countries according to scientific achievements. To our knowledge, attempts for systematic mapping health research output in the Eastern Mediterranean Region (EMR) are limited. Aims: We aimed to conduct a detailed bibliometric analysis of EMR biomedical and health research productivity during the period 2004-2013, considering country of first author. Methods: We applied an improved PubMed search strategy to obtain precise data on EMR research productivity, limiting articles to reviews, original research and case reports. Data were normalized to global research output, represented by total articles indexed in PubMed per year from 2004-2013, according to population size of each country. Second order polynomial trend lines were calculated and comparing 5-year periods: Results: Inspecting overall raw data, a clear increasing trend is observed. Regional share of global health related research ranged from 0.85-2.36% of total PubMed indexed publications during the study period. Five countries contributed to 80% of all published articles during study period; i.e., Islamic Republic of Iran (39%), Egypt (14%), Saudi Arabia (11%), Tunisia, and Pakistan (8% each). Overall, 2.35 articles are published per 100 000 population per year. While Kuwait maintained the highest per capita publication (followed by Tunisia, Lebanon, Qatar and Islamic Republic of Iran), Qatar, Islamic Republic of Iran and Saudi Arabia demonstrated the highest "per capita" population growth in publications. Three academic institutions accounted for over 10% of all publications that were led by an investigator from the Region. Collectively, most prolific 25 EMR institutions published 44% of all published biomedical and health research in the EMR. Conclusions: The overall global share of EMR health research publication is smaller than its global share of population or wealth. Biomedical and health research needs greater encouragement and supporting many EMR countries and/or institutions, especially those found to be least prolific in our analysis. The increase in academic publication on health has been more prominent in a few countries only. It is anticipated that the concentration of biomedical and health research in EMR academic institutions would help in translating knowledge into public health outcomes, if more suitable conditions are provided.