Approximately 10% to 30% of patients with ulcerative colitis and up to 70% of patients with Crohn's disease will undergo surgery at some point during their lifetime. Although patients with ulcerative colitis are considered "cured" by surgery, patients who have undergone an ileal pouch anal anastomosis may develop pouchitis, cuffitis, pouch irritability, or even Crohn's disease. Various therapies have shown success, including probiotics, in the prevention of pouchitis onset or relapse. Crohn's disease historically recurs following surgery; prophylaxis against disease recurrence has been attempted with a variety of agents, with variable success. Innovative therapies holding promise for the future treatment or prevention of these conditions are under exploration.