The bioactive component, amygdalin, was successfully separated from the crude extract of Prunus armeniaca L. using high-speed countercurrent chromatography (HSCCC) with high recovery. A polar two-phase solvent system, containing n-butanolethyl acetate-water (4 : 1 : 6, v/v/v) was run on a preparative scale. The lower phase was used as the mobile phase in the head to tail elution mode. A 208 mg quantity of the crude extract, containing 36.1% amygdalin, was loaded onto a 270 mL HSCCC column, which yielded 69 mg amygdalin of 98.7% purity with 90.7% recovery. The chemical structure of amygdalin was determined by electrospray ionization MS-MS and H-1 NMR.