Background: Several bibliometric analyses have been conducted in the Eastern Mediterranean Region (EMR), however, there is limited data from such analyses for the establishment of national or regional health research agenda. Aim: To assess the biomedical and health research outputs in EMR countries for 2004–2018 and their alignment with the regional strategic health priority areas identified by the WHO Regional Office for the Eastern Mediterranean. Methods: We searched and reviewed health-related articles indexed in PubMed and originating from EMR countries from 2004 to 2018 and used these as indicators of the country’s total biomedical research publication level. Data from a very large collection of over 300 000 articles were weighted to EMR’s contribution to the global research output. We used the mean and standard deviation to summarise the continuous variables and used frequencies and percentages to summarise the categorical variables. Results: Biomedical research publication in the EMR increased between 2004 and 2018. Five countries – Islamic Republic of Iran (43%), Egypt (14%), Saudi Arabia (11%), Pakistan (8%), and Tunisia (6%) – contributed 82% of all the publications, while the other countries contributed less than 4%. On average, EMR contributed 2.0% of the global biomedical research publications and 3.12 publications per 100 000 population for 2004–2018. Conclusion: Biomedical and health research publication increased unevenly across the EMR countries during the study period. Considering the complexity of the public health challenges in the region, there is a need for multidisciplinary and holistic approaches to health research to generate evidence for policy and to improve clinical and public health outcomes.