Colombia lacks experience in identifying health research priorities. A project for identifying health research priorities was begun in 2004 (meaning those arising from weighting and ordering health and disease problems which could be mainly resolved by research and knowledge). The Global Forum for Health Research combined matrix method, and other methods, was used as reference for developing projects and putting two main methodological paths into practice: designing and applying a method for qualitatively and quantitatively weighting and ordering health research problems and building consensus with researchers and scientific community representatives. Two national meetings, two regional meetings and a virtual forum were held for identifying predominant health problems. Once the predominant health problems had been identified (with the respective estimation of disease load), then they were evaluated by politicians and decision-makers and rated by basic science, clinical science and public health researchers in terms of making a contribution towards knowledge for facing, controlling or resolving such problems. Some health research priorities were obtained (by areas and others being overall priorities): chronic diseases, emergent infectious diseases, tuberculosis/leprosy, nosocomial infection and sexually transmitted diseases/HIV/AIDS.