A method of micellar electrokinetic capillary electrophoresis for determining the six flavonoids in Scutellariae Radix (i.e., baicalin, baicalein, wogonin 7-O-glucuronide, wogonin, oroxylin A 7-O-glucuronide, and oroxylin A) has been developed. The buffer solution (pH 7.24) composed of 20 mM sodium dodecyl sulfate (SDS), 20 mM sodium dihydrogen phosphate, and 25 mM sodium borate was found to be the most suitable electrolyte for the separation. The contents of the six flavonoids in crude Scutellariae Radix could easily be determined within about 15 min. On-column UV (254 nm) monitoring allowed the quantitative determination of baicalin. The effects of pH, surfactant concentration, and applied voltage on the migration behavior of the solutes were studied.