OBJECTIVE: To compare health research priority-setting methods and characteristics among countries in Latin America and the Caribbean during 2002 - 2012. METHODS: This was a systematic review that identified national health research policies and priority agendas through a search of ministry and government databases related to health care institutions. PubMed, LILACS, the Health Research Web, and others were searched for the period from January 2002 - February 2012. The study excluded research organized by governmental institutions and specific national strategies on particular disease areas. Priority-setting methods were compared to the "nine common themes for good practice in health research priorities." National health research priorities were compared to those of the World Health Organization's Millennium Development Goals (MDG). RESULTS: Of the 18 Latin American countries assessed, 13 had documents that established national health research priorities; plus the Caribbean Health Research Council had a research agenda for its 19 constituents. These 14 total reports varied widely in terms of objectives, content, dissemination, and implementation; most provided a list of strategic areas, suggestions, and/or sub-priorities for each country; however, few proposed specific research topics and questions. CONCLUSIONS: Future reports could be improved by including more details on the comprehensive approach employed to identify priorities, on the information gathering process, and on practices to be undertaken after priorities are set. There is a need for improving the quality of the methodologies utilized and coordinating Regional efforts as countries strive to meet the MDG.