Palatinose is a disaccharide present in honey, which has the characteristics of delayed digestion and absorption. We developed a palatinose-based balanced formula (PBF) and reported its beneficial effects on metabolic syndrome-related parameters in rats. To examine the effects of PBF in humans, we here conducted a crossover study using twenty-three subjects with impaired glucose tolerance. The subjects were divided into two groups: intervention to control (I/C) and control to intervention (C/I) groups. The I/C group consumed PBF (250 kcal) together with foods that were 250 kcal less than their usual breakfast (intervention meal) for the first 12 weeks, followed by their usual breakfast (control meal) for the last 12 weeks. The protocol for the C/I group was opposite in order: the control meal for the first 12 weeks, followed by the intervention meal for the last 12 weeks. In the first 12-week period, the intervention meal decreased 2-hr plasma glucose levels after 75-g oral glucose tolerance test (-15.7 +/- 20.1% change), while the control meal did not (0.8 +/- 31.6% change). The difference between these changes was significant (p = 0.038). The similar results were obtained from the comparison of the changes between the first and the last 12-week periods in the two groups combined (intervention vs control: -11.8 +/- 22.5 vs 11.2 +/- 30.2% change, p = 0.024). PBF also had the beneficial effects on serum free fatty acids levels and visceral fat area. In conclusion, PBF consumption has beneficial effects on metabolic syndrome-related parameters in humans.