HMRI has established seven research programs in:

• Brain and Mental Health;
• Cancer;
• Cardiovascular Health;
• Information Based Medicine;
• Public Health;
• Pregnancy and Reproduction; and
• Viruses, Infections/Immunity, Vaccines & Asthma (VIVA).

The strength of the HMRI Research Programs lies in the unique collaboration that brings together researchers from the University of Newcastle, Hunter New England Health and Calvary Mater Newcastle.

Hunter researchers are developing more effective diagnostic, treatment and preventative measures, translating scientific advances into better clinical practice, competitive commercial products and improved health care guidelines.

HMRI Research Programs receive infrastructure funding from the NSW Office of Science and Medical Research through the NSW Medical Research Support Program and the NSW Department of Health through the NSW Research and Development Capacity Building Infrastructure Grants Program. These funding programs support essential research infrastructure in the form of salaries, equipment and facilities, allowing the region to continue delivering quality research.

HMRI Research Programs also receive funding from charitable sources through the HMRI Foundation, PULSE and the Hunter Children’s Research Foundation (HCRF). The philanthropic funding supports HMRI project grants, scholarships, fellowships, travel grants and exchanges, and the HMRI awards for research excellence.

Researchers working in HMRI's programs are currently located at various health and medical research campuses around Newcastle including the University of Newcastle’s Callaghan Campus and David Maddison Building, John Hunter Hospital, Calvary Mater Newcastle, Mater Institute, James Fletcher Hospital and Wallsend Health Campus.