A double-blind crossover study using placebo and antibiotics effective against either aerobic or anaerobic organisms has been performed to elucidate the role of intestinal microflora in the pathogenesis of colonic pseudo-obstruction, which is now established as an important complication of jejunoileal bypass. Using strict Virginia Polytechnic Institute (VPI) technique, quantitative bacterial studies of the intestinal flora in the region of bypassed bowel have been correlated with symptoms of abdominal pain and distension. It has been shown that antibiotics effective against obligate anaerobes rapidly relieve the symptoms of pseudo-obstruction and this coincides with the disappearance of these organisms from this region of bowel. Symptoms rapidly recur when anaerobic organisms repopulate the bowel. It is concluded that obligate anaerobes may play a role in the pathogenesis of this complication.