More than 70% of clinicians presently use Kampo medicine. However, pharmacological studies on Kampo medicine, the characteristics of herbs, and their relations with intestinal microbiota in particular are insufficiently understood. Many of the main active ingredients of Kampo medicine are glycosides, a molecular group accounting for more than 10% of all Kampo medicine. Orally administered glycosides reach the lower digestive tract without being absorbed, and are then hydrolyzed by enteric bacteria, which utilize them as a food source. The aglycon they produce is absorbed into the body and becomes activated. The activation mechanism is altered by changes in the intestinal microbiota, and may also cause changes in this microbiota. For Kampo medicine, combined use with probiotics is expected, and Kampo medicine may act as a prebiotic itself. The concepts of "Sho" or "Kampo diagnosis" should also be considered based on differences in the intestinal microbiota.