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Objective Comparative evaluations of cellular toxicity, lipophilicity and in vitro transmembrane transport of eight cerebrovascular protection flavonoids including puerarin, rutin, hesperidin, quercetin, genistein, kaempferol, apigenin and isoliquiritigenin were investigated using rat blood-brain barrier (BBB) ceil, Caco-2 cell monolayer and everted intestine jejunm sac model.Methods The BBB bilayer was successfully co-cultured via rat brain microvascular endothelial cells and astrocytes.The apparent permeability coefficients (Papp) of the flavonoids were calculated from unilateral transport assays in Transwell system with simultaneous determination using a high performance liquid chromatography.The toxicity was determined by the MTT assay.Results The tested flavonoids exhibited time-dependent Papp values in these models, suggesting the transmembrane transport of these compounds by passive diffusion mode.There were some differences in the Papp of the active flavonoids between the BBB cell model and the Caco-2 cell model.The transport of the tested flavonoid could be enhanced when administrated with the flavonoid mixtures.The efflux mechanisms related with P-glycoprotein may exist with some flavonoids.The permeability was correlated to the parental skeleton, the number and position of glycoside and hydroxyl groups of the flavonoids.Conclusion These findings provided important information for establishing the transport relationship and predicting the oral bioavailability of the active flavonoids.