OBJECTIVE: To study the metabolism kinetics of baicalin and baicalein from Scutellaria baicalensis in rat liver microsomes and compare the effect of Banxiaxiexin-Decoction with different combinations on the metabolic activities of the flavonoids (baicalin and baicalein). METHODS: An UPLC method was developed for determination of baicalin and baicalein in rat liver microsomes incubation system. The effect of Banxiaxiexin-Decoction and different combinations (pungent-swelling group, bitter-descending group, sweet-invigorating group) on the metabolic activities of the flavonoids was investigated by vivo-induction and vitro-incubation method. RESULTS: The elimination of the flavonoids was linear, and the metabolism of baicalin had significant eliminated linear within 60 min, baicalein within 10 min. The peak area showed good linear relation when baicalin and baicalein was the concentration of 0.5 - 25 microg/mL. Microsomal protein concentration had significant effect on the flavonoids metabolism with the gradient from 0.2 g/L to 1.0 g/L in their corresponding time, and showed linear elimination with the growth of the concentration. The metabolic rate of baicalein in the blank liver microsomes was bigger than that of baicalin. The effect on metabolic of baicalin and baicalein, comparing the blank group, all parts showed inhibition strongest among the combinations, bitter-descending group second of that, pungent-swelling group had no significant for both, and sweet-invigorating group was without inhibition for baicalin, no significant inhibition for baicalein. CONCLUSION: Banxiaxiexin-Decoction shows inhibition on the metabolic for baicalin and baicalein, and is stronger than other combinations. This provides important pharmacological basis for compound prescription reasonable and clinical compatibility which plays the effect of mutual promotion.