| No. | Name of Institute | Approval Year | Supervisory Unit |
| 1 | Fujian Institute of E.N.T | 1996 | The First Affiliated Hospital |
| 2 | Fujian Institute of Abdominal Surgery | 1995 | The First Affiliated Hospital |
| 3 | Fujian Institute of Hypertension | 1996 | The First Affiliated Hospital |
| 4 | Fujian Institute of Orthopedics | 2000 | The First Affiliated Hospital |
| 5 | Fujian Institute of Neurology | 1995 | The First Affiliated Hospital |
| 6 | Fujian Institute of Ophthalmology | 1993 | The First Affiliated Hospital |
| 7 | Molecular Medicine Research Center of FJMU | 1993 | School of Basic Medical Sciences |
| 8 | Fujian Engineering Center of Reproductive Medicine | 1992 | School of Basic Medical Sciences |
| 9 | Fujian Institute of Ultrasonic Medicine | 2000 | The Affiliated Union Hospital |
| 10 | Fujian Institute of Hepatobiliary Surgery | 1996 | The Affiliated Union Hospital |
| 11 | Fujian Institute of Coronary Disease | 2000 | The Affiliated Union Hospital |
| 12 | Fujian Institute of Gerontology | 1998 | The Affiliated Union Hospital |
| 13 | Fujian Institute of Clinical Immunology | 1998 | The Affiliated Union Hospital |
| 14 | Fujian Institute of Endocrinology | 1994 | The Affiliated Union Hospital |
| 15 | Fujian Burns Institute | 1998 | The Affiliated Union Hospital |
| 16 | Fujian Institute of Neurosurgery | 2000 | The Affiliated Union Hospital |
| 17 | Fujian Research Center of Digestive Diseases | 1985 | The Affiliated Union Hospital |
| 18 | Fujian Institute of Cardiothoracic Surgery | 1997 | The Affiliated Union Hospital |
| 19 | Fujian Institute of Hemopathy | 1988 | The Affiliated Union Hospital |
| 20 | Fujian Research Center of Biomedical Engineering | 2003 | School of Pharmacy |
| 21 | Fujian Research Center of Drug’s Non-clinical Safety Evaluation | 2009 | School of Pharmacy |
