Autoimmune disorders occur when the immune system attacks the body's own cells. In Crohn's disease, these rogue immune cells attack the gastrointestinal system. The cause is unknown, but genetic factors seem to play a role.

Inflammation frequently occurs at the end of the small intestine that joins the large intestine, but the condition may affect any area of the digestive tract. As a result of the immune attack, the intestinal wall becomes thick, and deep ulcers may form.

The disease may occur at any age, but adolescence and early adulthood are the periods of highest risk. Other risk factors include a family history of Crohn's disease and Jewish ancestry. About 7 out of every 100,000 people will develop Crohn's disease.