Fructooligosaccharide (FOS) is a typical prebiotic agent. A randomized, double-masked, placebo-controlled study was performed to evaluate the prebiotic effect of daily intake of an isotonic solution containing FOS on body weight gain and the reduction of diarrhea in children in an urban slum in Bangladesh over six consecutive months. We enrolled a total of 150 children, aged 25-59 months. Sixty-four children in the FOS group received 50 mL of isotonic solution with 2 g of FOS added, and 69 children in the placebo group were given an identical solution with 1 g of glucose added, once a day. The measurement of body weight was carried out every other day; height and arm circumference were measured once a month; and the children‘s mothers were interviewed to obtain data about diarrhea, the consistency and constitution of stool, other symptoms, and antibiotic treatment. As a result, the body weight gain during the six-month period was 0.86±0.55 kg in the FOS group and 0.89±0.48 kg in the placebo group, while the increase in height and arm circumference were not significantly different between the two groups. The number of diarrhea episodes during the six-month period was not significantly different. A significant reduction in the duration of diarrhea days and of duration per episode was observed in the FOS group (p=0.039 and p=0.008, respectively). In conclusion, daily intake of FOS was associated neither with the children‘s growth nor with the number of diarrhea episodes, but a significant reduction in the duration of diarrhea days was observed. Further studies are needed to confirm the effects of FOS by changing the doses and eliminating the influence of antibiotics.