In order to develop a selective membrane separation process for flavonoids, i.e. baicalin, baicalein and flavone extracted from a crude drug, "Wogon", We have measured the permeabilities of these flavonoids through a polyvinyl alcohol membrane, together with their aqueous solubilities. The aqueous solubilities of baicalin and baicalein increase with increasing aqueous solution pH due to the acid dissociation of the saccharic carboxyl group of baicalin or the phenolic hydroxyl group of baicalein, The mass transfer coefficients of flavonoids experimentally obtained in both systems of single and mixed constituents agreed well with the calculated values based on a solution-diffusion model together with the acid dissociation of the carboxyl or hydroxyl groups of baicalin and baicalein, respectively. The selective mutual separation of flavonoids can be achieved from mixed solution of constituents in the neutral pH region. Furthermore, a quantitative discussion of the permeation behavior of flavonoids through the PVA membrane is provided from a molecular modelling computational viewpoint.