Ileal pouch anal anastomosis (IPAA) is associated with complications in a significant number of patients, including ileal-anal separation, anal stricture, pouchitis, pelvic sepsis, and small bowel obstruction. In most cases, these complications may be successfully treated using either medical or surgical therapy and do not result in long-term pouch dysfunction. Important preventative measures include accrual of experience or creation of a team with experienced surgical leadership and scrupulous selection of patients who have no features of Crohn's disease. Despite these precautions, 5% to 15% of patients will develop chronic pouch dysfunction and pouch failure requiring diversion with or without excision of the pouch. Medical measures, such as antibiotics, immunomodulators, and biologic agents, and surgical measures such as advancement flap anoplasty may be attempted to salvage pouch function and are successful in more than 50% of cases. Indeterminate colitis does not preclude IPAA; however, Crohn's colitis is absolute contraindication for same. Patients who require colectomy and are suspected for any reason to have CD may undergo ileorectal anastomosis with preservation of anorectal continence and excellent functional results.