A simple, comprehensive and efficient capillary electrophoresis method using a dual cyclodextrin system was developed for the simultaneous determination of seven isoflavones (3 '-methoxypuerarin, puerarin, 3 '-hydroxypuerarin, ononin, daidzin, daidzein and genistin). Baseline separations of the seven isoflavones were achieved within 11 min with the running buffer consisting of 35 mm sodium tetraborate, 9.0 mm sulfobutylether-beta-cyclodextrin and 30 mm alpha-cyclodextrin at pH 9.34, and peaks were detected at 254 nm. Other separation parameters included the separation voltage for 15 kV and the working temperature for 25 degrees C. Under the optimum conditions, good linearities were obtained with linear correlation coefficients of seven isoflavones of 0.9978-0.9992. The limits of detection and the limits of quantification were 0.7-2.9 and 2.5-9.5 mu g/mL, respectively. Excellent precision and accuracy were obtained. The intraday and interday precision ranged from 0.7 to 2.0% and from 0.8 to 1.9%, respectively. The recoveries of seven analytes were from 97.7 to 103.1%. This method was successfully applied to determine the seven analytes in Radix Puerariae and its preparations.