Here, we look at the impact of the scientific production of Brazilian research institutions. Data were collected from SciVal and InCites for governmental research institutions (state and federal), and then we focussed on the two largest: Embrapa (Agriculture) and Fiocruz (Health). Institutions in the area of health, environment and physics tended to show higher impact than other areas, those in physics showed low first, last and corresponding authorships (<20%). Health institutions had a high profile in Policy and Patents, especially abroad, while agriculture had a more local impact. Citations in policy documents increased impact by 220%. Brazilian institutions in Defence, Agriculture, Energy & Nuclear, and Economic areas generally perform below world means. While some institutions may show a higher impact on specific indicators, the present study raises the need for an in-depth analysis of these institutions and their return on investments. Information contained here can help these institutions in strategic planning to improve impact results, including the uptake of science by the Brazilian government. While Fiocruz seems to meet this demand, Embrapa still needs to reaffirm its space within the system. Discussion on the return on investment (monetary and other resources) made in institutions these institutions require future studies.