Ileal mucosal morphology, fecal bacteriology, fecal volatile fatty acids, and their interrelationships were studied in 15 patients with an ileal pouch-anal anastomosis and 14 patients with an ileostomy after proctocolectomy for ulcerative colitis. Pouch effluent, compared with ileostomy effluent, had a greater ratio of anaerobes to aerobes (p less than 0.05), and greater numbers of Bacteroides (p less than 0.01) and Bifidobacteria (p less than 0.05). Fecal volatile fatty acids, products of anaerobic bacterial fermentation, were also increased in pouch effluent compared with ileostomy effluent (propionate, p less than 0.05; butyrate, p less than 0.01). Mucosal change in the pouches showed no significant correlation with frequency of defecation, completeness of emptying, or pouch design, but the degree of villous atrophy was correlated with the number of Bacteroides (rs = 0.93, p less than 0.01) and with fecal butyrate (rs = 0.68, p less than 0.05). Fecal propionate was significantly correlated with the percentage of stool retained after defecation (rs = 0.82, p less than 0.01). These findings indicate that the bacterial ecology of ileal pouches has an important influence on the morphology of their mucosal lining.