Four flavonoids, chrysin, baicalein, baicalein-7-O-glucoside, baicalein-7-O-diglucoside (Oroxylin B) and one unknown flavonoid have been isolated and purified for the first time in the seeds of Oroxylum indicum by high-speed counter-current chromatography with a two-phase solvent system composed of chloroform-methanol-water (8:10:5, v/v). Then, 50 mg baicalein-7-O-glucoside, 10.5mg baicalein-7-O-diglucoside, 4.5mg chrysin-7-O-diglucoside, 25 mg baicalein and 45 mg chrysin could be obtained after injecting 20 mg/ml sample extract ten times and their purities were 96, 90, 85, 95 and 98%, respectively. All these constituents were identified by high-performance liquid chromatography–mass spectrometry and nuclear magnetic resonance.