Blue honeysuckle fruits are rich in anthocyanins with many beneficial effects such as reduction of the risk of cardiovascular diseases, diabetes and cancers. High-speed counter-current chromatography (HSCCC) was used for the separation of anthocyanin on a preparative scale from blue honeysuckle fruit crude extract with a biphasic solvent system composed of tert-butyl methyl ether/n-butanol/acetonitrile/water/trifluoroacetic acid (2:2:1:5:0.01, v/v) for the first time in this paper. Each injection of 100 mg crude extract yielded 22.8 mg of cyanidin 3-glucoside (C3G) at 98.1% purity. The compound was identified by means of electro-spray ionisation mass (ESI/MS) and 1H and 13C nuclear magnetic resonance (NMR) spectra. © 2013 Elsevier Ltd. All rights reserved.