Flavonoid contents of nine raw and nine commercial propolis samples were analyzed by capillary electrophoresis. At first, 15 commercially available flavonoid standards including apigenin, chrysin, luteolin, galangin, kaempferol, morin, myricetin, quercetin, quercitrin, rutin, hesperetin, naringin, naringenin, daidzein and genistein were used to develop the electrophoretic conditions. At a running temperature of 25°C and detection wavelength at 214 nm, the separation of these standards was most satisfactorily achieved by a combination of capillary zone electrophoresis (CZE), utilizing 0.1 M borate buffer (pH 9.5) containing 5% methanol under a voltage of 18 kV, and micellar electrokinetic capillary electrophoresis (MECC), utilizing 0.03 M sodium borate (pH 8.5) containing 0.05 M SDS under a voltage of -15 kV. We found 12 out of the 15 flavonoids were identified in raw propolis, but only 11 were detected in commercial propolis products. The total contents of the identified flavonoids in raw and commercial propolis were 254 to 19147 ppm and 1228 to 7985 ppm, respectively, suggesting that both the origin and processing are important factors affecting the flavonoid content in propolis.