Crohn's disease is a chronic disorder that causes inflammation of the digestive or gastrointestinal (GI) tract. Patients with Crohn's disease have an immune system that mistakes food, bacteria, and other materials in the intestine for a foreign substance. The immune system reacts by attacking the intestine. This reaction causes chronic inflammation which leads to ulcerations and bowel injury.

Although it can occur anywhere in the gastrointestinal tract, Crohn's disease commonly affects the end of the small intestine (the ileum), and the colon. Crohn’s disease may also cause inflammation of the rectum and anus. In Crohn's disease, all layers of the intestine may be involved, but normal healthy bowel may exist in close proximity to unhealthy bowel.