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The Office of Health Affairs manages four statewide programs funded by the State of California and one program funded by a grant from The California Wellness Foundation. The state-funded Special Research Programs, which include the Universitywide AIDS Research Program (UARP), the Breast Cancer Research Program (BCRP), the Tobacco-Related Disease Research Program (TRDRP), make awards to scientists within the University of California and in external organizations throughout California. The Academic Geriatric Resource Program (AGRP), which is also funded by the State of California, and The California Wellness Foundation/University of California Wellness Lectures Program, a program funded by The California Well Foundation through March 1998, limit their awards to University of California faculty.

The administration of the Special Research Programs is largely the same across programs, especially with regard to the development of and adherence to a rigorous and competitive peer review of grant proposals. Program staff work closely with a policy advisory board to determine research priorities, which are used to develop calls for applications that are broadly distributed to California's diverse scientific community. Using the National Institutes of Health peer review system as a model, the program staff develop and manage a competitive review process that brings together scientists with appropriate expertise to assess the scientific merit of each proposal. The breast cancer and AIDS programs include non-scientist advocates in this process. The results of this peer review process are provided to the program's advisory committee, which makes funding recommendations. Once these recommendations have been approved, the program staff make awards to the selected Principal Investigators and, in the cases of the UARP, BCRP, and TRDRP, they manage multi-year grants in accordance with their respective established policies and procedures.