Crohn disease favors the ileum (the lower part of the small intestine) but can occur anywhere along the intestinal tract while, by contrast, ulcerative colitis affects the colon (the large intestine) alone. The inflammation in Crohn disease involves the entire thickness of the bowel wall, whereas in ulcerative colitis the inflammation is confined to the mucosa (the inner lining) of the intestine.

The symptoms of IBD include abdominal pain and diarrhea. The course is typically unpredictable. Symptoms tend to wax and wane, and long remissions and even the spontaneous resolution of symptoms are well known. The disease can be limited to the intestine or affect the skin, joints, spine, liver, eyes, and other organs. Although people of any age can have inflammatory bowel disease, the diagnosis is most commonly first made in young adults.

Intestinal ulcers and bleeding are common in both Crohn disease and ulcerative colitis. But complications such as intestinal strictures (narrowings), fistulas, and fissures (tears) are far more common in Crohn disease than in ulcerative colitis.

Small intestinal bacterial overgrowth in Crohn disease can result from an intestinal stricture and is treated with antibiotics. Crohn disease of the duodenum and jejunum can cause malabsorption of nutrients can cause malnutrition, weight loss, and diarrhea. In Crohn disease of the ileum, malabsorption of bile salts can cause diarrhea and malabsorption of vitamin B12 can lead to anemia.

There is an increased risk of colon cancer in ulcerative colitis. Yearly monitoring with colonoscopies and biopsies of the colon for premalignant cells and cancer is recommended for patients after 8 to 10 years of chronic inflammation of the colon.