Chemical identification of the compounds in human urine following administration of the traditional Chinese medicines, Daisaiko-to and Shosaiko-to (Dachaihu-tang and Xiaochaihu-tang in Chinese, respectively), was achieved by using a linear relationship between the logarithm of the capacity factor, log k', and that of the volume fraction of CH3CN, log X(s)(vol), in the aqueous mobile phase: -log k'=A+B log X(s)(vol). Comparison of the slope, B, and the intercept, A, between the urinary compound and its suspected authentic specimen gave satisfactory results in the chemical identification. We applied this method to the initial stage of pharmacokinetic studies on the herbal medicines and identified seven flavonoids and two anthraquinone derivatives in the urine specimens obtained after herbal administration.