Peak tailing and nonalkaloid coelution usually hinder alkaloid purification. In this study, a 2DLC, strong cation exchange (SCX) coupled with positively charged RP (PGRP) LC, was developed to overcome these problems. Ten compounds including basic and nonbasic compounds were analyzed. Nonbasic compounds, which are coeluted with basic compounds on RP or PGRP columns, were weakly retained on the SCX column. In addition, a symmetrical peak shape (tailing factors <1.2) of basic compounds can be obtained in the current system. Compared to two other 2D systems, the current system provided the highest orthogonality (R(2) = 0.045). Furthermore, the SCX coupled with PGRP system was applied for alkaloid purification from a traditional Chinese medicine. Nineteen alkaloids were obtained and one of them was identified as a novel compound. The overall results demonstrate that the proposed system is a powerful tool for alkaloid purification. CI - (c) 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.