The effects of flavonoids on caffeine N3-demethylation, a marker activity of CYP1A2, in human liver microsomes were investigated to elucidate the inhibition mechanism and the structure-activity relationship. Caffeine N3-demethylase activity was inhibited by the presence of various flavonoids, whose structures seem to be closely related to the degree of inhibition. Among twenty-one compounds tested, the most active was chrysin with an IC50 value of 0.2 microM. Others had IC50 values ranging from 1 to more than 500 microM. Kinetic analysis revealed that the mechanism of inhibition varied among the flavonoids. The inhibitory effect was postulated to be governed by factors such as the number of hydroxyl groups and glycosylation of these free hydroxyl groups. An increase in the number of free hydroxyl groups reduced the inhibitory effect on P450 activity. Analysis of the quantitative structure-activity relationship (QSAR) showed that the volume to surface area ratio was the most effective factor on the inhibition of caffeine N3-demethylation, and the electron densities on the C3 and C4' atoms exercised significant influence on the inhibitory effect. The calculated inhibitory effect of flavonoids on CYP1A2 activity was highly correlated with the antimutagenicity of flavonoids in 2-amino-3,4-dimethylimidazo[4,5-flquinoline (MelQ)-induced umu response.