Approximately 20-30% of patients with ulcerative colitis would eventually require surgery despite recent advances in medical therapy. Ileal pouch-anal anastomosis has become the surgical treatment of choice after total proctocolectomy. A subset of patients who had a preoperative diagnosis of ulcerative colitis may develop Crohn's disease or a Crohn's disease-like condition of the ileal pouch after surgery. Diagnosis, differential diagnosis, and management of Crohn's disease of the ileal pouch have been challenging. A combined approach with the assessment of clinical history, endoscopy, histology, abdominal/pelvic imaging, and examination under anesthesia is necessary for an accurate diagnosis, disease classification, management and improvement in outcome. A multidisciplinary approach with gastroenterologists, colorectal surgeons, gastrointestinal pathologists and radiologists for proper medical, endoscopic, and surgical treatment is advocated.