Although the biotransformation of ginsenosides in gastrointestinal tract has been extensively studied, very less is known about the hepatic cytochrome P450 catalyzed metabolism. The major aims of this study were to clarify the metabolic pathway and involved CYP isoforms,and to explore the structure metabolism relationship of, protopanaxatriol (PPT) type ginsenosides in hepatic microsomes. Efficient depletion of ginsenoside Rh1, Rg2, Rf, and PPT was found, whereas the elimination of Re and Rg1, characterized with a glucose substitution at C20 hydroxy group, was negligible, in microsomal incubation systems. Based on a LC/MS-IT-TOF analysis, the oxygenation metabolism on the C20 aliphatic branch chain was identified as the predominant metabolic pathway of PPT ginsenosides in both human and rat hepatic microsomes. By comparing with authentic standards, the C24-25 double bond was identified as one of the oxygenation site to produce the metabolites of C20-24 epoxide (ocotillol-type ginsenosides). Both chemical inhibition and human recombinant CYP isoforms assay indicated that CYP3A4 was the predominant isozyme responsible for the oxygenation metabolism of PPT ginsenosides. Enzyme kinetic evaluations in rat and human hepatic microsomes and human recombinant CYP3A4 isozyme incubation systems reached a generally consistent result in that the intrinsic clearance ranked as Rf≤Rg2<Rh1<PPT, closely correlating with their Log P values and the number of glycosyl substitutions. Results obtained from this study suggest that CYP3A4 catalyzed oxygenation metabolism plays an important role on the hepatic disposition of ginsenosides, and that the glycosyl substitution, especially at C20 hydroxy group, determines their intrinsic clearances by CYP3A4.