HEI is a public private partnership established to research and provide impartial information about the health effects of emissions from motor vehicles and other sources of environmental pollution. HEI receives half of its core funds from the EPA and half from twenty-eight manufacturers or marketers of motor vehicles or engines in the US.

The HEI research program has addressed many important questions about the health effects associated with exposure to both regulated pollutants such as carbon monoxide, ozone, and nitrogen dioxide, and unregulated pollutants such as diesel exhaust, aldehydes, and methanol. HEI has also funded studies to understand the mechanisms of diseases, to develop better methods to assess health effects and determine dose response relationships. The program has included theoretical, in vitro, animal, controlled human exposure, and epidemiological studies.

The center has had three priority research areas: Mobile Source Air toxics - which includes research on benzene and 1,3-butadiene, mechanisms of carcinogenicity and biomarkers of dose and effect, and the health effects of aldehydes; Oxygenated Fuels - the comparative metabolism and health effects of ethers used to increase gasoline oxygen content (MTBE); and Particles - health effects of particulate air pollution and potential relationship to increased daily mortality.