Gastrodia elata Blume is a famous Chinese medicinal plant, which has been widely used for the treatment of rheumatism, epilepsy, paralysis, hemiplegia, lumbago, headache and vertigo. High-speed counter-current chromatography was successfully used for the first time for the preparative isolation and purification of the bioactive component gastrodin from G. elata Blume. The crude gastrodin was obtained by extraction with ethanol from the dried roots of G. elata Blume under sonication. Preparative high-speed counter-current chromatography with a two-phase solvent system composed of n-butanol-ethyl acetate-water (2:3:5, v/v/v) was successfully performed yielding 48 mg gastrodin at 96% purity from 500 mg of the crude extract (10.3% gastrodin) with the recovery of approximately 90% in a one-step separation.