Background: Yacon is a root crop which contains high amounts of fructooligosaccharides (FOS). The aim of this study was to investigate the effects of yacon syrup on colon transit time in healthy volunteers. Methods: In a placebo-controlled, double-blind study yacon was administered to 16 healthy individuals (8 males, 8 females) in a dose of 20 g daily (equal to 6.4 g FOS) in a 2-week crossover design. Each period was interrupted by a 2-week wash-out phase. Transit time was assessed by a radio-opaque marker technique. Results: Transit time (mean ± SEM) through the gastrointestinal tract was significantly decreased from 59.7 ± 4.3 to 38.4 ± 4.2 h (p < 0.001). Yacon was well tolerated with an excellent side effect profile. Bloating is not an uncommon side effect observed with FOS, but bloating-related disturbances were not significantly more often reported with yacon compared to placebo. Stool frequency increased from 1.1 ± 0.1 to 1.3 ± 0.2 times per day and the consistency showed a tendency for softer stools as assessed by a numerical depicted stool protocol. Neither parameter did, however, reach statistical significance. Conclusion: Yacon markedly accelerates colonic transit in healthy individuals. Further studies are needed in constipated patients to confirm these preliminary data. Due to the low caloric content of yacon, the root could be a useful treatment in constipated diabetics or obese patients.