A physical examination, taking a full history and blood tests may provide useful clues, but looking inside the bowel with the use of an endoscope (colonoscopy) and taking tissue samples for further examination in the laboratory is an important diagnostic tool used to investigate IBD.

Barium X-ray may also be needed to detect abnormalities and to investigate those parts of the gastrointestinal tract that cannot be reached by the endoscope. Other tests may also be required.

Despite all these tests being performed, it can sometimes be difficult to diagnose Crohn's disease. There is usually no delay in finding ulcerative colitis.