Sixteen IgA-deficient German Shepherd Dogs with small intestinal bacterial overgrowth were randomized into 2 groups. One group was fed a chicken based kibble diet; the other was fed the same diet, but with 1% fructo-oligosaccharides supplemented at the expense of cornstarch. After being exposed to the diets for 46 to 51 days, the group that ate the supplemented diet had significantly (P = 0.04) fewer aerobic/facultative anaerobic bacterial colony-forming units in fluid from the duodenum/proximal part of the jejunum, as well as in the duodenal mucosa. We could not detect significant differences in the species of bacteria found in the intestine of these 2 groups of dogs. We conclude that at least some dietary carbohydrates can affect small intestinal bacterial populations in dogs with small intestinal bacterial overgrowth.