Approximately 30% of patients with ulcerative colitis will eventually require surgery. Ileal pouch-anal anastomosis has become the surgical treatment of choice in ulcerative colitis patients with refractory disease or dysplasia who require proctocolectomy. A subset of patients with ileal pouches may develop Crohn's disease or a Crohn's disease-like condition of the pouch after the surgery. Diagnosis and management can be challenging. A combined assessment of endoscopy, histology, radiographic imaging and examination under anesthesia is often necessary for an accurate diagnosis, disease classification, management and prognosis. A multidisciplinary approach by a medical and surgical team, together with experienced pathologists and radiologists, is advocated.