Microscopic changes in duodenal biopsy specimens from 16 elderly patients with small-bowel bacterial overgrowth were studied before and after cyclical courses of antibiotic treatment, using computer-aided morphometry measurements as well as visual assessment. Twenty-three subjects in the same age group with no evidence of intestinal disorder were studied as controls. Mean villus height was significantly reduced in the pre-treatment study compared to the post-treatment measurements and those in controls. Similar significant differences were found in mean crypt depth and total mucosal thickness. The mean intra-epithelial lymphocyte count was raised before treatment and fell after treatment to a level similar to that of the controls. The mean lymphocyte count in the peripheral blood rose significantly after treatment. This study provides objective evidence of microscopic structural changes in the bacterial overgrowth syndrome in old age. The return to normality after antibiotic treatment suggests that these changes are directly attributable to the presence of bacteria in the gut lumen.