Commonly in Crohn's disease and rarely in ulcerative colitis, injury to the bowel from the inflammation and ulceration can result in complications.

In Crohn's disease, inflammation and scarring can narrow or obstruct the intestine making it too small for digested food or faeces to pass through. Small breaks in the bowel wall can also occur, resulting in the development of abscesses and fistulas. These are abnormal channels that connect between loops of bowel or to other hollow organs opening out of the body (bladder, vagina), allowing stool to leak through. They can also track through from the bowel to the skin surface.

Abscesses and fistulas are often found in the perianal region. In severe, acute ulcerative colitis, severe bleeding, perforation (open break of the bowel wall) or toxic megacolon (ballooning out of the bowel) can occur. People with ulcerative colitis over many years have a higher risk of developing cancer of the bowel, especially if not treated.