Chlorogenic acid, an ester formed between caffeic acid and quinic acid, is a major phenolic compound in the traditional Chinese medicinal herb Flos Lonicerae. The separation and purification of chlorogenic acid from the crude extract of Flos Lonicerae was achieved by high-speed counter-current chromatography (HSCCC). A high acid, highly polar two-phase solvent system containing n-butanol-acetic acid-water (4:1:5) was run on a preparative scale. The upper phase was used as the mobile phase in the head to tail elution mode. A 300-mg quantity of the crude extract containing 5.97% chlorogenic acid was loaded on a 342-ml HSCCC column. Double separations were performed with the same solvent system yielding 16.9 mg chlorogenic acid at 94.8% purity with approximately 90% recovery.