Aloin, naturally a mixture of two diastereoisomers, aloin A and aloin B, is the major anthraquinone in aloe, and now served as one of the important control constituents in most of the commercial aloe products. High-speed countercurrent chromatography (HSCCC) combined with silica gel column chromatography was developed for the preparative separation of the two individual aloins. Aloin A (98%) and aloin B (96%) were obtained. Fast atom bombardment mass spectrometry (FAB-MS), 1H nuclear magnetic resonance (1H NMR) and GOESY (gradient-enhanced nuclear Overhauser effect spectroscopy) were employed for the elucidation of their structure conformation. The developed method is of high preparative capacity and high efficiency in resolution.