Micellar electrokinetic chromatography (MEKC) conditions were developed to analyze the constituents of Scutellariae Radix (SR) and Scutellaria baicalensis roots. Using the MEKC method, the major flavonoid constituents of baicalin, baicalein and wogonin of wild and cultivated S. baicalensis roots were compared. In a preliminary comparison of electropherogram, one special peak was found in a wild sample but not in a 2-year-cultivated one. The compound corresponding to the peak was isolated and identified as a phenylethanoid glycoside, acteoside, by comparing the 1H- and 13C-NMR spectral data with that of the authentic compound. This is the first time acteoside has been isolated from the Scutellaria genus. It could only be found in SR derived from wild S. baicalensis roots and 4-year-cultivated plants, but not in plant materials cultivated for 3 years. Applying the MEKC method established in this study, rapid and simultaneous determinations of acteoside together with 3 flavonoids in samples were achieved. The method can thus be used for the quality control of SR in a shorter analysis period than HPLC.