In public health systems, priority setting in health research determines resource allocation to produce evidence and proposals aimed at solving the population's health problems. In Cuba, the Science and Technical Division (S&T) of the Ministry of Public Health (MINSAP) leads this process, based on the country's health policy framework and consistent with optimal use of resources. To set health research priorities (HRPs) for 2010, a three-stage interpretive method was used involving 215 professionals working at all levels of the health system in 14 territories, 22 MINSAP experts, and academic administrators and health system managers at provincial and national levels. In Stage I, HRPs were identified and confirmed in each territory using a nominal group technique and ranked using the Hanlon Method. Further classification, ranking and ratification in Stages II and III resulted in a final set of five HRPs defined in the annual Request for Proposals from which projects are selected for funding. Results reflected consensus on the need to prioritize research on determinants of low risk perception and on program management. The participatory process laid the groundwork for conducting research better designed to contribute to solutions to major health problems affecting the Cuban population.