Background Brazil invests more in scientific research than any other Latin American country. Its Ministry of Health is a source of funding for research, along with other development agencies, and its Department of STDs, HIV/AIDS and Viral Hepatitis is one of the agencies that most strongly supports and promotes research in the field of STDs/HIV/AIDS in Brazil. However, it remained to be seen whether or not effective use is being made of scientific evidence during public health policy formulation and if it is being used to validate the government’s decision-making process. The purpose of this study was to assess the use of scientific evidence produced by projects funded by the Department.

Methods An exploratory study was carried out that surveyed former directors of the Department. Questions were asked concerning the Department’s institutional mission, support for research and technological development, use of the results of research projects, and use of these projects’ scientific evidence during public health policy formulation.

Results Analysis of the data showed that the Department has promoted and encouraged research studies and technological development, in partnership with centres for excellence in research, institutes of higher education, and national and international development agencies, and has funded 220 projects since 2004, resulting in 1,198 scientific publications. Despite these contributions to advances in scientific knowledge, the present study showed that incorporation of scientific evidence was limited to research the Department had specifically requested, such as economic and strategic analyses and studies on operational programmes.

Conclusion Strategies for integrating science-based evidence with its practical application should be identified. Science-based evidence should be disseminated, promoted and incorporated into the process of developing public health policies, strategies, and practises.