Surgery can become necessary if the drug treatment is no longer effective or if a complication develops. Most people with Crohn's disease require surgery at some stage, most commonly to remove a severely affected portion of the intestine. Unfortunately, surgery in Crohn's disease does not result in a cure.

Only a small number of people with ulcerative colitis require surgery, but when performed, the most common procedure involved results in a cure.

In both conditions where an operation requires complete removal of the colon and rectum, a permanent stoma (intestinal opening) is brought out on the abdomen. A procedure for an internal pouch is available for people with ulcerative colitis.