BACKGROUND: Defining health technology assessment priorities has been a challenge for the Department of Science and Technology who adopted a prioritization criteria strategy (epidemiologic relevance, services/policy relevance, state of the art, operational feasibility and social demand) for demands from MoH technical areas. However, evaluation demands do not always correspond to health needs. OBJECTIVES To analyze the relationship between projects financed from 2003 to 2013 and disease burdens in Brazil. METHODS Systematization of the summaries from financed projects through searches in the information from www.saude.gov.br/rebrats and http://pesquisasaude.saude.gov.br/bdgdecit/ and categorization according to the twenty sub-groups of diseases and injuries of disease burden (Dalys) research in Brazil (SHARMM ET al, 1998). RESULTS CONCLUSIONS The percentage found allows for the questioning of the prioritization starting point where the criteria are applied to subjects selected due to external influence and pressure from the market and not necessarily based on the needs impacting the population’s health. Uniting the two dimensions while also taking into account the strategic innovations in order to prioritize and finance assessment will be important for health systems sustainability.