A method based on capillary electrophoresis with electrochemical detection was developed for the determination of puerarin, daidzein and rutin. Effects of several important factors such as the acidity and concentration of running buffer, separation voltage, injection time, and detection potential were investigated to acquire the optimum conditions. The working electrode was a 300-microm diameter carbon disc electrode positioned opposite the outlet of capillary. The three analytes could be well separated within 12 min in a 40 cm length capillary at a separation voltage of 9 kV in a 50 mmol/l borate buffer (pH 9.0). The relationship between peak currents and analyte concentrations was linear over about three orders of magnitude with detection limits (SIN=3) ranging from 0.241 x 10(-6) to 0.511 x 10(-6) mol/l for all compounds. This proposed method demonstrated long-term stability and reproducibility with relative standard deviations of less than 5% for both migration time and peak current (n=7). It has been successfully applied for the determination of puerarin, daidzein and rutin in Chinese traditional drugs, the vines of Pueraria lobata (Wild.) Ohwi and Puerariae Radix.