The University of Otago's Faculty of Medicine comprises of departments from three regions: Dunedin, Christchurch, and Wellington. Each region contains eight core departments of the same name, while Dunedin and Christchurch also have certain region-specific departments.
- Faculty of Medicine Te Kaupeka Whaiora
- Centre for Rural Health Te Pokapū Whaiora ki Tuawhenua
- Dunedin
- Department of Bioethics
- Department of Medicine Te Tari Whaiora
- Department of Obstetrics and Gynaecology Oranga Wahine
- Department of Paediatrics and Child Health Te Tari Matai Mate me te Hauora Tamariki
- Department of Pathology and Molecular Medicine
- Department of Primary Health Care
- Department of Psychological Medicine Te Tari Whakaora Hinengaro Tangata
- Department of Public Health
- Department of Surgery and Critical Care Te Tari Hāparapara, Te Tari Whāomoomo
- Christchurch
- Department of Māori/Indigenous Health Innovation (MIHI)
- Department of Medicine Te Tari Whaiora
- Department of Obstetrics and Gynaecology Te Tari Mātai Whakawhānau me ngā āhua Wāhine
- Department of Orthopaedic Surgery and Musculoskeletal Medicine Te Tari Hāparapara me te Whaiora Ua-kāhiwi
- Department of Paediatrics and Child Health
- Department of Pathology and Molecular Medicine
- Department of Primary Health Care
- Department of Psychological Medicine Te Tari Whakaora Hinengaro Tangata
- Department of Public Health
- Department of Surgery and Critical Care Te Tari Hāparapara, Te Tari Whāomoomo
- Wellington
- Department of Medicine Te Tari Whaiora
- Department of Obstetrics and Gynaecology
- Department of Paediatrics and Child Health Te Tari Matai Mate me te Hauora Tamariki
- Department of Pathology and Molecular Medicine Te Tari Whai Mokoroa, Rongoā Rāpoi Ngota
- Department of Primary Health Care
- Department of Psychological Medicine Te Tari Whakaora Hinengaro Tangata
- Department of Public Health Te Tari Hauora Tūmatanui
- Department of Surgery and Critical Care Te Tari Hāparapara, Te Tari Whāomoomo