Isomaltulose is a disaccharide in which glucose is α- 1,6 linked to fructose. The capacity of fasted Malaysian adults to tolerate boluses of isomaltulose (25 g, 50 g, 75 g, 100 g) was investigated by serial measurements of breath hydrogen. A response of > 20 ppm was considered to indicate spill-over of isomaltulose to the colon. Twenty-eight consenting participants [10 males, 18 females, 20 - 36 years of age, with body mass index (BMI) ranging from 15 – 31 kg/m2] underwent crossover studies using a portable apparatus over five hours. 9/25 (36 %) participants gave evidence of spill-over at 75 g and 19/28 (70 %) to 100 g of isomaltulose. In 6 males and 11 females, glycaemic responses were compared to sucrose with a two-week washout period. The blood glucose response to isomaltulose (6.6 ± 0.9 SD mmol/L) was significantly lower than to the same bolus of sucrose (8.7 ± 1.8 SD mmol/L; p = 0.001). Faecal pH changes were measured to test for possible prebiotic effects. After a bolus of 75 g of isomaltulose, the acidity of both the first and second subsequent faecal samples was significantly greater than pre-test samples, suggesting that isomaltulose may possess a prebiotic potential. The finding of intolerance to isomaltulose suggests that caution should be exercised in its use as a carbohydrate nutrient.