The creation of a pelvic ileal reservoir is associated with inflammatory changes in the reservoir mucosa. Chronic inflammation and villous atrophy are seen in most patients with both ulcerative colitis and familial adenomatous polyposis (FAP), the two prime indications for the operation. The mucosa undergoes a form of colonic metaplasia which is demonstrable by morphological, mucin histochemical, immunohistochemical and proliferation methods. Other pathological features such as mucosal ischaemia, mucosal prolapse, granulomas and pyloric metaplasia are seen in the pouch mucosa and these changes contribute to the confusion over definitions of pouchitis. The term pouchitis denotes a chronic relapsing inflammatory condition of the reservoir which occurs in 10-20% of patients and is one of the more severe long-term complications of reservoir construction. Useful definitions of pouchitis should include clinical, endoscopic and histopathological criteria. There are close associations between pouchitis and an original diagnosis of ulcerative colitis. The cause of pouchitis is currently obscure but there is evidence to suggest it may represent a recurrence of colitis in metaplastic mucosa and may provide a useful human model for colitis. The demonstration of markedly increased proliferative activity in association with colonic metaplasia has worrying connotations. However, dysplasia has not yet been described in colitic reservoirs and very few adenomas have been seen in polyposis reservoirs. Nevertheless the clinical and pathological evidence would indicate that long-term surveillance of the reservoir mucosa by endoscopy and mucosal biopsy is warranted.