Background There is a wide range of intellectual work written about health research, which has been shaped by the evolution of diseases. This study aims to identify the leading journals over the last 25 years (1990–2014) according to a wide range of bibliometric indicators. Methods The study develops a bibliometric overview of all the journals that are currently indexed in Web of Science (WoS) database in any of the four categories connected to health research. The work classifies health research in nine subfields: Public Health, Environmental and Occupational Health, Health Management and Economics, Health Promotion and Health Behavior, Epidemiology, Health Policy and Services, Medicine, Health Informatics, Engineering and Technology, and Primary Care. Results The results indicate a wide dispersion between categories being the American Journal of Epidemiology, Environmental Health Perspectives, American Journal of Public Health, and Social Science & Medicine, the journals that have received the highest number of citations over the last 25 years. According to other indicators such as the h-index and the citations per paper, some other journals such as the Annual Review of Public Health and Medical Care, obtain better results which show the wide diversity and profiles of outlets available in the scientific community. The results are grouped and studied according to the nine subfields in order to identify the leading journals in each specific sub discipline of health. Conclusions The work identifies the leading journals in health research through a bibliometric approach. The analysis shows a deep overview of the results of health journals. It is worth noting that many journals have entered the WoS database during the last years, in many cases to fill some specific niche that has emerged in the literature, although the most popular ones have been in the database for a long time. Electronic supplementary material The online version of this article (doi:10.1186/s12992-016-0186-4) contains supplementary material, which is available to authorized users.