ISCIII is a public legally autonomous body under the direct supervision of the Spanish Ministry of Health and Consumer Affairs (MSC, after its name in Spanish), whose main activities include the promotion of biomedical and other health science research.

ISCIII manages the National Programme of Biomedicine and the National Programme of Technology for Health and Welfare through the Fund for Health Research (FIS, in Spanish), which is its extramural research-funding branch. In 2006, the FIS committed € 130 million to fund basic, applied and translational research on a competitive basis upon public calls.

ISCIII has been entrusted by the MSC to manage the National Program for Rare Diseases and has been funding 12 networks within this program for a total budget of € 20 million over 3 years.

The IIER is a branch of ISCIII integrated into the Deputy General Directorate for Co-ordination of Applied Services, Training and Research, together with the Microbiology, Environmental Health, Tropical Medicine and Epidemiology National Centres.