In this study, baicalin, as a marker substance of Scutellariae Radix, was quantitatively analyzed by a high performance liquid chromatography-photodiode array detector (HPLC-DAD). We identified wogonoside, baicalein, and wogonin in the Scutellariae Radix by a high performance liquid chromatography-electrospray ionization-mass spectrometer (HPLC-ESI-MS). The baicalin was separated on a Xterra C18 column (5 ㎛, 4.6 x 250 ㎜) using mobile phase consisting of 38% acetonitrile in 0.68% phosphoric acid. The baicalin spectrum in the Scutellariae Radix extracts was coincided by comparing with UV-visible spectrum (200-550 ㎚) of baicalin standard in the library. The amount of baicalin in Scutellariae Radix was 10.46%, which is higher than KFDA’s guideline. The marker substances of Scutellariae Radix showed a strong base peak [M]+ in the positive detection mode following as; baicalin (m/z; 271 [MH+-sugar]+, 447 [M+H]+), wogonoside (m/z; 285 [MH+-sugar]+, 461 [M+H]+), baicalein (m/z; 271 [M+H]+), wogonin (m/z; 285 [M+H]+). These results are consistent with the fragment pattern and molecular weight of standard components from literature.