NASA operates two major in-house research labs in California: the Ames Research Center in Moffett Field (1700 employees) and the Dryden Flight Research Center in Edwards (400 employees). Both conduct mostly aeronautics R&D. DOD, as noted in the industry section, has the largest network of federal labs in California. Together these labs performed $1.4 billion in R&D in FY 1993.

Although their funding represents not much more than a blip at the national level, California is home to several world-renowned nonprofit research centers that receive funds from the federal government. SRI International, headquartered in Menlo Park, received $64 million in mostly DOD funds for R&D in its California labs. The Scripps Clinic and Research Foundation in La Jolla received $73 million in FY 1993 for its medical research, almost entirely from HHS. Two other institutions in La Jolla, the Salk Institute and the La Jolla Cancer Research Foundation, received $34 million and $12 million respectively, again mostly from HHS. In Santa Monica, the RAND Corporation received $12 million, mostly from HHS, for R&D conducted in organizational units outside the FFRDCs it manages.