Xanthohumol (XN), a prenylated chalcone, has been proposed to have beneficial effects on human health, including antimicrobial activity. To clarify whether the exposure to XN has an impact on the composition of the intestinal microbiota, 100 mg XN/kg body weight was given daily to rats for 4 wk. Diversity of the fecal microbial community was analyzed using PCR-DGGE. Although intact XN was detected in the feces of the rats at a concentration of up to 2.3 mg/g fecal dry weight, major shifts in the PCR-DGGE patterns in response to this flavonoid were not observed. The similarity index decreased slightly from 70 to 62% for the XN-treated rats and from 71 to 63% for the untreated animals. Thus, changes in the rat fecal microbiota observed in the course of the XN application are most likely due to intraindividual variability. However, the water content of the feces increased significantly during the XN treatment period.