Chinese herbs nephropathy (CHN) is a kind of severe kidney disease caused by excessively taking aristolochic acid (AA). Hence, it is essential for health security and quality control of related herbal medicines to develop an efficient method for separation and determination of these two important components in Traditional Chinese Medicines. In this study, a rapid capillary zone electrophoresis (CZE) method using 120 mM sodium borate buffer containing 10 mM beta-cyclodextrin (beta-CD) as modifier was firstly developed for the analysis of AA-I and AA-II within 4min in some medicinal plant samples. The separation conditions including pH of running buffer, CD content in the buffer system, applied voltage and capillary temperature were systematically optimized, and two kinds of aristolochic acids in 37 herbal samples of Aristolochia plants were successfully determined with high separation efficiency, satisfactory sensitivity, repeatability and recovery. The result indicated high variability in the contents of aristolochic acids due to different species and regions. The comparison of CZE method with high performance liquid chromatography (HPLC) was also discussed.