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This study examined the relationship between the metabolism of the constituents of herbal medicines by human intestinal microflora and the level of metabolites excreted in the urine. This was performed by administering Chungpesagantang (CST) to volunteers and measuring their fecal metabolic activity CST to and urine excretion of daidzein, one of the metabolite of CST. The metabolic activity of of CST dadizein was 54.8 ± 16.7 mmol/h/g wet feces. When CST was administered orally to the subjects, the amount of daidzein excreted in the urine over 24 h was 103.7 ± 55.8 mg, which accounted for 20.2% of the puerarin, daidzin and daidzein contained in CST. However, neither puerarin nor daidzin were excreted in the urine. The profile of daidzein excreted in the urine was found to be in proportion to that of the metabolic activity of the CST components. This suggests that the daidzein level excreted in the urine of the subjects administered CST is associated with the daidzein glycoside-hydrolyzing activity of the fecal microflora.