High-speed countercurrent chromatography (HSCCC) was successfully used to isolate three bioactive compounds, i.e., amygdalin from bitter almond and taxifolin-3-glucoside and quercetin-3-galactoside (hyperoside) from water extract of Agrimonia pilosa Ledeb, respectively. From 1 g of the crude extract 65 mg of amygdalin was isolated at 97% purity using a two-phase solvent system composed of ethyl acetate-n-butanol-water (5:2:5, v/v) by preparative HSCCC. From a 400 mg amount of crude extract of Agrimonia pilosa Ledeb, 11 mg of taxifolin-3-glucoside and 8 mg of hyperoside were isolated at 96% purity using a two-phase solvent system composed of ethyl acetate-methanol-water (25:1:25, v/v) similarly by preparative HSCCC. The final structural identification was performed by MS, (1)H-NMR and (13)C-NMR Spectra.