To understand the role of intestinal microflora in the biological effect of functional herbs, which have been used in Korea, Japan, and China as traditional medicines, and suggest new bioactive compounds transformed from herbal constituents, the metabolic activities of the functional herb components (ginsenoside Rb1, crocin, amygdalin, geniposide, puerarin, ginsenoside Re, poncirin, hesperidin, glycyrrhizin, and baicalin) toward their bioactive compounds (compound K, crocetin, benzaldehyde, genipin, daidzein, ginsenoside Rh1, ponciretin, hesperetin, 18b-glycyrrhetic acid, and baicalein) were measured in fecal specimens. The metabolic activities of these components were 882.7 +/- 814.5, 3,938.1+/- 2,700.8, 2,375.5 +/- 913.7, 1,179.4 +/- 795.7, 24.6 +/- 10.5, 11.4 +/- 10.8, 578.8+/- 206.1, 1,150.0+/- 266.1, 47.3 +/- 58.6, and 12,253.0 +/- 6,527.6 mmol/h/g, respectively. No differences were found in the metabolic activities of the tested components between males and females, although these metabolic activities between individuals are extensively different. The metabolites of functional herb components showed more potent cytotoxicity against tumor cells than nonmetabolites. These findings suggest that intestinal microflora may activate the pharmacological effect of herbal food and medicines and must be the biocatalytic converter for the transformation of herbal components to bioactive compounds.