Enteric microflora were studied in relation to carbohydrate tolerance in 50 infants with severe diarrhea. During the acute stage, 16 infants tolerated lactose, 23 patients had a specific lactose intolerance, eight had a generalized disaccharide intolerance, and three had monosaccharide intolerance. All patients had bacterial proliferation in the small intestine. A linear increase in the bacterial counts in duodenal aspirates (3 to 105) was observed with an increasing severity of carbohydrate intolerance. The least bacterial growth (mean 103) was found in the lactose tolerant infants. A moderate growth occurred in patients with specific lactose (104-5) and disaccharide (106) intolerance; and a severe infection (108) in those with monosaccharide intolerance. Seven patients, who developed a more severe carbohydrate intolerance after a period of diarrhea, had an increase in their bacterial count as well. After recovery from diarrhea, the bacterial counts of the duodenal aspirates decreased and all patients rapidly recovered the capacity to tolerate all carbohydrates. The types of bacteria grown were similar in all patients: klebsiella species most often, then Escherichia coli (nonpathogenic), enterococci, pseudomonas and proteus species. A mixed flora was often present. In 24 patients, the bacteria isolated from the small intestine were different from those found in the feces. The proliferation of bacteria within the small bowel of infants with diarrhea may be related to the presence of undigested carbohydrates.