The Department of Gastrointestinal Surgery is the largest in the country in terms of strength, skills and experience. The department is recognized for training surgeons for the Fellowship Examination of the Royal College of Surgeons of Edinburgh.

This department has performed the first living donor liver transplantation in Kerala. (More details in 'Organ Transplantation')

The following divisions exist in this department:

Hepatobiliary and Pancreatic Surgery: The center is the largest pancreatic surgery unit in the country. Liver resections and surgery for bile duct tumours as well as biliary structures are performed regularly. 

Intestinal surgery: Treatment of diseases of stomach and intestine, including specialized operations for colitis and GI fistula.

Laparoscopic surgery: The unit has pioneered development of laparoscopic surgery. All forms of basic and advanced laparoscopic surgery for diseases such as gallstones, appendicitis, hernia, splenic disease, intestinal obstruction, liver cysts, pancreatic disease, reflux esophagitis and hiatus hernia are performed using state-of-the-art equipment. 

A coloproctology division deals with all problems of the large intestine and anus. This is one of the largest centers for treatment of "piles".