Crohn's disease may cause sores, or ulcers, that tunnel through the intestine and into the surrounding tissue, often around the anus and rectum. These abnormal tunnels, called fistulas, are a common complication of Crohn's disease and may become infected. Crohn's disease can also cause anal fissures, which are narrow tears that extend from the muscles that control the anus (anal sphincters) up into the anal canal.

An anal fistula can often be treated with medications, though sometimes surgery to repair the fistula may be necessary. Conservative treatment, including antibiotics and medications to reduce pain and inflammation, is usually tried before surgery. Surgery for an anal fistula, which is usually done only in cases of complications such as an abscess, sometimes results in persistent nonhealing.

Anyone with an unusual anal fistula that does not respond to conservative treatment should be examined for Crohn's disease, since a fistula is often the first sign of Crohn's disease. An examination may include anoscopy or sigmoidoscopy, procedures that allow a health professional to view the lower rectum and lower large intestine through a viewing scope. Complete evaluation may require sedation because examination of the area can cause discomfort.