A simple and rapid capillary zone electrophoresis method was developed for the separation of the main alkaloids from Sophora flavescens Ait. with the optimum buffer solution containing 110 mM NaH2PO4 and 15% 2-propanol (pH 3.0). The field-amplified sample stacking (FASS) technique was applied to the on-line concentration of the alkaloids. The data presented in this work demonstrate that the use of a short water plug at the column inlet is essential for improving the reproducibility of FASS with electro-injection, and that the water plug injection time affected the sensitivity significantly. The sample concentration was further increased by about 2-3-fold by the introduction of a relatively longer water plug. With this stacking measure, the concentration sensitivity was about 3-4 orders of magnitude higher than in hydrodynamic injection.