Introduction. Crohn's Disease causes inflammation of the bowel. It most commonly affects the lower small intestine (ileum) and the large intestine (colon), but may involve any part of the digestive tract from the mouth to the anus.The inflammation extends through the entire thickness of the bowel wall.ntroduction. Crohn's Disease causes inflammation of the bowel. It most commonly affects the lower small intestine (ileum) and the large intestine (colon), but may involve any part of the digestive tract from the mouth to the anus.