Jejunal bacterial flora, bile acid deconjugation, and breath hydrogen and methane excretion were studied in nine patients with end-to-side and nine patients with end-to-end jejunoileostomy and in eight patients with gastric bypass. Bacterial numbers did not differ significantly between healthy controls and any of the patient groups. Production of fermentation gases in anaerobic cultures supplemented with carbohydrates did not occur with jejunal secretions from healthy controls but was found in all intestinal bypass patients and half the gastric bypass patients. Bacterial bile acid deconjugation activity was significantly higher in end-to-side compared with end-to-end jejunoileostomy patients. In gastric bypass patients bile acid deconjugation was not significantly affected. Breath hydrogen after glucose ingestion was abnormal in six patients with end-to-side and three with end-to-end jejunoileostomy and in six of the patients subjected to gastric bypass. The highest values were found in the later group. Breath methane, which is found in one third of a healthy population, was absent in all 18 patients with intestinal bypass, and this may indicate that a change occurs even in the colonic microflora after this operation. Both intestinal and gastric bypass may change the small-bowel microflora, with the greatest changes occurring after end-to-side jejunoileostomy and the least changes after gastric bypass.