To determine the effect of CHO concentration in infant formula on tolerance and macronutrient absorption, we studied 12 lactose-intolerant males (age x±SD 5.7±2 mo) with chronic diarrhea and malnutrition. In 2 successive metabolic balances infants received a semi-elemental formula that contained high CHO (HCHO) (9.1 g/dl) or low CHO (LCHO) (6.7 g/Dl). Formulas were isocaloric; the difference in CHO content was counterbalanced by the amount of fat. Breath was collected for H2. Fecal fat, osmolality, N, and energy were determined and energy-derived from fecal CHO was calculated. Mean daily caloric intake was not significantly different between the 2 periods (x±SD was 114±26 vs 117±28 kcal/kg/d; HCHO vs LCHO, respectively). No significant difference was seen between the 2 periods in: wt gain/g body wt during the 3 d of each balance, peak H2 levels, fecal N, and osmolality. LCHO formula was tolerated better than HCHO as shown by a significantly lower stool output (x±SD 387±230 g vs 764±443, respectively, [p<0.05]), higher fecal pH (p<0.05), and lower amount of fecal CHO determined at bedside (p<0.05), Macronutrient absorption was also better during the ingestion of LCHO formula as shown by significantly lower amounts of total fecal energy, lower CHO excretion (p<0.05), and a better coefficient of fat absorption (p<0.001). CHO content had an overriding effect on nutrient absorption and formula tolerance in infants with severe chronic diarrhea.