In view of the importance of short-chain fatty acids (SCFA) for the colonic epithelial function and their possible relation with the reported spontaneous regression of rectal polyps after subtotal colectomy with ileorectal anastomosis, we compared the SCFA concentrations in faeces of five familial adenomatous polyposis (FAP) patients before, and in 10 FAP patients after operation to each other and to those of 10 healthy controls. Anaerobe cultural counts and concentrations of organic acids were also investigated in the same faecal samples from FAP patients and controls. The preoperative cultural counts were not significantly different from those of the controls. After colectomy, the Bacteroides (P < 0.002; P < 0.02), and bifidobacteria counts (P < 0.02; P < 0.005) were decreased compared to controls and untreated FAP patients. The ratio of acetic acid to total SCFA significantly increased, which coincided with a proportional decrease of the other SCFA. The frequently observed regression of rectal polyps after colectomy cannot be explained from these results. One would rather expect a possible stimulation of polyp growth and dedifferentiation of colonic epithelial cells.