The teaching departments of the Faculty of Medicine are Anaesthesia, Anatomy, Biochemistry, Pharmacology, Physiology, Microbiology, Pathology and Immunology, Medicine, Surgery, Obstetrics and Gynaecology, Paediatrics, Psychological Medicine, Social and Preventive Medicine, Community Medicine and Forensic Medicine. In addition the faculty has established a Unit of Medical Informatics and research centres including the Institute for Reproduction and Development, the Centre for Early Human Development, the Centre for Molecular Biology and Medicine, the Centre for Bioprocess Technology and the Centre for Mothers' and Children's Health. The faculty also has strong links with research institutes such as the Baker Medical Research Institute (Alfred Hospital), The Prince Henry's Institute for Medical Research (Monash Medical Centre), the Mental Health Research Institute (Royal Park Hospital), and the MacFarlane Burnet Centre for Medical Research (Fairfield Hospital).
The academic operations of the faculty are governed by the faculty board. The dean is the chairperson of faculty board and has administrative responsibility for the faculty. As head of the faculty, the dean is assisted with administrative matters by the faculty manager and administrative officers. Assistance with academic matters is provided by the associate deans and the assistant dean. Teaching in the hospitals and other clinical settings is coordinated through the offices of the clinical subdeans and the hospital clinical deans. Heads of departments and directors of centres and institutes provide academic leadership within their disciplines and are responsible for the management of staff and resources. Heads and directors together with all other professors play a significant role in the overall academic activities of the faculty.