High-speed counter-current chromatography (HSCCC) and preparative high-performance liquid chromatography (prep-HPLC) were successively used for the separation of epigallocatechin and flavonoids from Hypericum perforatum L. The two-phase solvent system composed of ethyl acetate-methanol-water (10:1:10, v/v) was used for HSCCC. About 900mg of the crude extract was separated by HSCCC, yielding 7.8mg of quercitrin at a purity of over 97%, 12.6mg of quercetin at a purity of over 93%, and 38.9mg of a mixture of hyperoside, isoquercitrin and miquelianin constituting over 97% of the fraction. A mixture of epigallocatechin and avicularin pooled from three HSCCC runs, a total amount of 54.3mg, was further separated by prep-HPLC yielding 23.4mg of epigallocatechin and 15.3mg of avicularin each at a purity of over 97%.