Mucosal morphology and faecal bacteriology were studied in 30 patients with ileoanal anastomosis and J-pouch and 10 patients with conventional ileostomy. Patients with ileoanal anastomosis had more acute and chronic inflammatory changes on histological examination than patients with conventional ileostomy. Patients with ileoanal anastomosis had a greater number of anaerobes and total bacteria and a greater ratio of anaerobes to aerobes in faecal samples than patients with conventional ileostomy. Patients with a history of clinical pouchitis had more acute inflammation than those without. In patients with ileoanal anastomosis there was a significant correlation between acute inflammation and number of aerobes and between chronic inflammation and number of anaerobes and total bacterial counts. These observations suggest that bacterial overgrowth in the pouch may be a possible pathogenic factor in inflammatory changes in the mucosa.