Five flavonoids (catechin, hyperoside, quercitrin, quercetin, and rutin) were separated and determined by capillary electrophoresis with electrochemical detection. Effects of several important factors, such as the pH and concentration of running buffer, separation voltage, injection time, and detection potential were investigated to determine the optimum conditions. The five flavonoids were baseline separated within 20 min in a 60 cm length capillary at a separation voltage of 19.5 kV with a running buffer consisting of 60 mmoL/L Na2B4O7 - 120 mmoL/L NaH2PO4 (pH = 8.8). The relationship between peak current and analyte concentration was linear over about two orders of magnitude with detection limits (S/N = 3) ranging from 0.02 to 0.05 microg/mL for all compounds. This method was successfully used to determine the above five flavonoids in Agrimonia pilosa Ledeb. with relatively simple extraction procedures, and the assay results were satisfactory.