A method based on capillary electrophoresis with electrochemical detection (CE-ED) was developed for the determination of baicalein, baicalin and quercetin in Scutellariae Radix and its pharmaceutical preparations. The effects of some important factors such as the acidity and concentration of running buffer, separation voltage, injection time, and the potential of working electrode were investigated to acquire the optimum condition. The working electrode was a 300-mum 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 the separation voltage of 12 kV in a 100 mmol l(-1) borate buffer (pH 9.0). The response was linear over three orders of magnitude with detection limits (S/N=3) ranged from 0.224 to 0.548 mumol l(-1) for all three analytes. This proposed method demonstrated good long-term stability and reproducibility with R.S.D. of less than 5% for both migration time and peak current (n=7). It has been successfully applied to analyze the actual samples with satisfactory assay results.