Introduction - A methanolic extract from Gentianella amarella ssp. acuta was shown to contain several xanthones exhibiting acetylcholinesterase inhibitory activity. These xanthones were difficult to separate by conventional LC techniques, which prevented the isolation of pure compounds in sufficient amounts to perform in-depth biological testing. Objective - To develop a suitable preparative method for the separation of closely related xanthones. Methodology - The methanolic extract was first partitioned with solvents of increasing polarity, in order to separate glycosides from xanthone aglycones. High-speed countercurrent chromatography (HSCCC) methods were then optimised for the fractionation of both polar and non-polar extracts. Results - The use of HSCCC enabled the separation of xanthones which co-eluted by HPLC. Ten closely related xanthones- three of which were isomeric-were successfully isolated by developing suitable solvent systems. All compounds were obtained in sufficient amounts to allow further biological assays (e.g. up to 250 mg), including even minor compounds that were not detectable by analytical HPLC. Conclusion - The orthogonality of HSCC with HPLC and the absence of solid-phase supports enabled the detection, separation and preparative isolation of closely related compounds which were difficult to resolve by other techniques. Copyright (C) 2008 John Wiley & Sons, Ltd.