When Crohn's disease first begins, or during a flare-up, you might experience: 1  Abdominal pain, usually at or below the navel. 2  It is typically worse after meals. 3  Diarrhea that may contain blood. 4  Sores around the anus. 5  Drainage of pus or mucus from the anus or anal area. 6  Pain when you have a bowel movement. 7  Mouth sores.