Restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) is currently the procedure of choice for ulcerative colitis patients who require colectomy. Despite its wide acceptance, a variety of long-term complications of the procedure exist that can be severe and even lead to pouch excision. Pouchitis occurs in up to one half of patients after IPAA, but is usually well controlled with medical therapy. A small percentage of patients develop chronic persistent pouchitis, which often requires long-term medical therapy and may result in pouch failure. Fistulas and strictures can also complicate the pouch procedure. In general, patients with Crohn's disease are not usually offered IPAA, because recurrence of disease, fistulas, abscesses, and strictures may lead to a higher incidence of pouch failure. Some ulcerative colitis patients develop complications after IPAA and are subsequently diagnosed with Crohn's disease. These patients may develop refractory fistulas, strictures, and extraintestinal manifestations of inflammatory bowel disease. Neoplastic transformation of the pelvic pouch has also been reported, particularly in patients with chronic pouchitis. Thorough follow-up and endoscopic surveillance with biopsies of the ileal pouch are therefore recommended.