Abstract: OBJECTIVE To establish the high performance capillary electrophoresis (HPCE) fingerprint chromatogram of genuine Polygalae Radix from Shanxi and get the control chromatogram. METHODS The separation was carried out in an uncoated fused silica capillary (75 μm×57 cm, effective length 50 cm). The running voltage was 18 kV. The buffer was 20 mmol·L^-1 Na₂B₄O₇ containing 25% methanol, and the wavelength was 210 nm. Data and chromatogram were dealt with “Computer Aided Similarity Evaluation” software in order to analyse the similarity of fingerprint chromatogram of Polygalae Radix from different districts. RESULTS The control fingerprint of HPCE of Polygalae Radix was established, and the similarity of fingerprint chromatogram of Polygalae Radix from different districts were compared. CONCLUSION This method is proved to be simple, rapid and accurate, and can be used as a new method for the quality control of Polygalae Radix.