A simple, accurate and reproducible Capillary electrophoresis (CE) assay has been developed for the determination of baicalin, baicalein, wogonin and chrysin in Scutellaria baicalensis. Successful separation of these compounds has been obtained in 35 mM phosphate butter (pH 7.0) using a untreated fused silica capillary ($57{;}cm{ imes}75{;}{mutextrm{m}}$ i.d.) at $25^{circ}C$ with the electric field of 19kV. Baicalin, baicalein wogonin and chrysin was separated and detected at 280 nm 13 min. The detection limits of CE were acceptable compared to HPLC. Reproducibilities of migration time and peak area were 0.66~1.11% (within-run), 2.18~3.38% (between-run) and 3.50~4.55% (within-run), 3.97~4.82%(between-run) at CE. The results indicate that CE could be a promising technique for quality and quantity control analysis of Scutellaria baicalensis as a validation method.