Traditional Chinese Medicines (TCM) have attracted great interest in recent researchers as alternative medicines for incurable diseases. This review focuses on qualitative and quantitative analytical approaches for bioactive metabolites of components flavonoids and saponins of traditional Chinese medicines by TLC system, although various methods have been introduced. Emphasis will be put on the processes of metabolite extraction from intestinal bacterial cultures or urines, separation (mobile phase) and detection. The identified metabolites by selection of extraction solvent and detection methods are also discussed. In addition, metabolite determinations of flavonoids (baicalin, apiin, rutin, quercetin, quercitrin, kaempferol, diosmin, hesperidin, poncirin, naringin, puerarin, daidzin, daidzein, tectoridin) and saponins (ginsenosides, kalopanaxsaponins, glycyrrhizin, chiisanoside, saikosaponins, soyasaponins) in culture fluid, in urine and in some herbal formula extracts are summarized. These bioactive metabolites of these components by intestinal microflora should be connected to pharmacological actions.