The challenge of providing quality while maintaining costs at affordable levels for society has motivated the implementation of health system reforms in various countries, seeking “allocative efficiency”, namely, prioritizing actions with the best cost-effectiveness ratio. This situation assigns increasing value to the adoption of evidence-based practices and policies. In Brazil, however, there was a persistent mismatch between scientific output and the use of its results in defining health policies and services. The Department of Science and Technology (DECIT), strengthened by the creation of the Secretariat of Science, Technology, and Strategic Inputs under the Ministry of Health in 2003, has contributed to identifying and promoting strategic research for the SUS. The main guidelines for the work by DECIT are provided by the National Agenda for Research Priorities in Health and the National Policy for Science, Technology, and Innovation in Health (PNCTIS), both approved during the 2 nd National Thematic Conference in 2004. The Conference included extensive involvement by health researchers, professionals, managers, and users of the National Health System (Guimaraes R, et al., Cad Saude Publica 2006; 22:1775-94). Participation by SUS managers has been crucial for including health problems on the scientific research agenda. An example is the growing participation by State health departments in the management of the Research Program for the SUS, implemented in all States of Brazil financed by DECIT and State Foundations to Support Research. The presence of the DECIT in the national coordination of health research has also allowed Brazil to establish multicenter studies and collaborative networks that require broad dialogue among many stakeholders. The Longitudinal Study on Adult Health (ELSA) and the National Networks for Clinical Research and Cell Therapy are examples of this exercise, demonstrating maturity in the management of health research investments. From 2003 to 2009, DECIT financed more than 3,700 research projects and made available R$650 million in funds, 60% of which from its own budget and the rest from partner institutions. In the area of specialized care, the strengthening of the scientific basis for incorporating products and services into the SUS requires serious attention, without which the system’s sustainability will be in jeopardy. Considering the need to guarantee the Constitutional right to health, the high costs of new diagnostic and therapeutic techniques, and the growing recourse to court injunctions by users of the SUS to ensure their access to treatment and medicines, decisions by health managers at the 3 levels of government must be backed by cost-effectiveness and cost-utility estimates. In this sense, the creation of the Commission for the Incorporation of Technologies by the Ministry of Health in 2006, the consolidation of the Division for Health Technology Assessment under DECIT, the establishment of the Brazilian Network for Health Technology Assessment (REBRATS), and the approval of the Technology Management Policy in the SUS are important initiatives. Specifically, DECIT has already issued three calls for research projects on health technology assessment and hired 278 studies. These efforts notwithstanding, much remains to be done. In the current context, perhaps the main challenge is to define an organizational structure to promote technology research and assessment in the SUS, ensuring the continuity and extension of the actions under way. Dealing with this challenge requires participation not only by health managers, professionals, and community representatives of social control in the SUS, but also by members of the scientific community.