Crohn's disease may result in fistulas. A fistula is an abnormal connection between two areas. These are thought to form when inflammation extends into the area surrounding the bowel wall. Fistulae can develop between two GI organs (for example, the small intestine and the large intestine), between GI organs and the bladder, between GI organs and the vagina, and between GI organs and the skin. The most common location for these fistulae is, again, the ileum (the last part of the small intestine). A unique kind of fistula in Crohn's disease is a perianal fistula, which connects the inside lining of the rectum (the last part of the colon) with the skin surrounding the anus.

Depending on which organs are connected by fistulae, patients can have different symptoms. Fistulae between the small and large intestine can cause diarrhea or passage of undigested foods. Fistulae between the intestine and bladder can result in urinary tract infections, with symptoms of burning with urination, cloudy urine, or blood in the urine. Fistulae to the vagina can result in passage of gas or stool through the vagina. Finally, fistulae to the skin can initially present as a painful bump or boil (called an abscess) that then opens up and drains fluid or stool. To treat fistulae, there are medical options (if there is also a significant amount of inflammation, oftentimes including antibiotics) and surgical options (especially if strictures recur frequently).