Research faces the challenge of balancing relevance to decision making and excellence in the strict adherence to the norms of scientific inquiry. This paper examines the organizational responses that can be undertaken to promote integration of these potentially conflicting goals. We posit that there seem to be structural barriers to effective communication between researchers and decision makers, such as differences in priorities, time management, language, means of communication, integration of findings and definition of the final product of research. These barriers must be overcome through solutions aimed at the organization of research. In this respect, there are three possible models to approach the tension between excellence and relevance: academic subordination, segregation and integration. Only the latter makes it possible to reconcile the advantages of proximity to decision making with the procedures to assure academic quality. In addition to organizational design and institutional development, a strategy to promote research must include a set of incentives to prevent the 'internal brain drain', that is, the tendency of researchers to move to managerial positions. There are four guiding principles to address this problem: parallel careers, academic autonomy, administrative sacrifice and inverted incentives. The complexities of health problems demand that we create new organizational formulas to finally balance relevance and excellence in research.