Fecal bile acids (FBA) were analyzed by gas-liquid chromatography in 29 patients [17 with ulcerative colitis (UC) and 12 with adenomatosis coli (AC)] and 5 healthy volunteers. Seven UC and 9 AC patients had undergone total colectomy and J-shaped ileal pouch-anal anastomosis (JAA). The mean daily FBA output was similar for JAA and terminal ileostomy patients (approximately 370 mg/day), and was about 1.5 times that of healthy Japanese volunteers (approximately 235 mg/day). The output of unconjugated bile acids, secondary bile acids, and 7-dehydroxylated bile acid was higher in JAA patients with UC than in terminal ileostomy patients, but there were no significant differences between the groups. The total fecal bacterial count in JAA patients was 10 times that in terminal ileostomy patients but was 1/10 of that in healthy volunteers. In patients with defunctioning high ileostomy, FBA output increased markedly (maximum, 3054 mg/day), and serum cholesterol levels were also significantly lower (P less than 0.05). These results suggest that after JAA the bile acid metabolism and fecal bacterial flora undergo more normalization than after terminal ileostomy.