Clinical activity at ISMETT is organized across multiple departments.

There are currently five departments with corresponding units:

• Department of Anesthesia and Intensive Care (Director: Dr. Antonio Arcadipane).
• Department for the Treatment and Study of Abdominal Diseases and Abdominal Transplantation (Director: Salvatore Gruttadauria)
• Department for the Treatment and Study of Pediatric Abdominal Diseases and Abdominal Transplantation (Director: Jean de Ville de Goyet)
• Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation (Director: Michele Pilato)
• Department of Diagnostic and Therapeutic Services (Director: Angelo Luca)