Abstract The adaptive response of the large bowel to surgical defunction in man is essentially unknown, although in the rat there is progressive hypoplasia and a reduced propensity to experimental carcinogenesis. Mucosal biopsies were taken from the upper rectum completely defunctioned by a proximal stoma from 2 months to 5 years earlier in 11 patients and from 14 controls without abdominal operations or disease. Samples were established in organ culture and, after 16 h, crypt cell production rate (CCPR) was determined by a stathmokinetic technique. Crypt morphometry was also undertaken. CCPR in defunctioned large bowel was less than half that of controls: (mean (s.d.) 1.96 (0.68) versus 4.65 (0.54) cells crypt−1 h−1, P <0.0001). Likewise, crypt length was 24 per cent lower (0.34 (0.05) versus 0.44 (0.04) mm, P <0.0001) and crypt width was 38 per cent lower (0.04 (0.01) versus 0.07 (0.01) mm, P <0.0001). Rectal defunction causes profound and persistent hypoplasia in man.