Proctocolectomy with ileal pouch-anal anastomosis is the surgical treatment of choice for severe chronic ulcerative colitis and familial polyposis coli because the entire colonic mucosa is removed while anal function can be preserved and the necessity for permanent ileostomy is eliminated. Long-term functional results are generally gratifying, as defecation frequency and degree of incontinence are acceptable in most patients. Pouchitis, however, a non-specific inflammation of the ileal reservoir, is a major long-term complication occurring in a considerable number of patients. The etiology of pouchitis is unknown. Since pouchitis occurs more frequently or even exclusively in ulcerative colitis patients it is assumed that pouchitis is a novel manifestation of inflammatory bowel disease. However, bacterial overgrowth in the ileal pouch may also play a pathogenetic role. Chronic inflammation and villous atrophy of varying severity is found in virtually all pouches. Acute inflammatory changes and ulceration are associated with pouchitis.