Health research systems in the Eastern Mediterranean Region are not well developed to generate and use knowledge to improve health, reduce inequity and contribute to economic development. This study aimed to provide core data on National Health Research Systems (NHRS) in 10 Eastern Mediterranean countries in order to inform actions to strengthen health research system governance and management. Whilst there were examples of good practice, few countries had a formal NHRS and many basic building blocks needed for an effective system had not been put in place. Although limited in focus, the study provides useful information for countries to initiate action to strengthen their NHRS.