OBJECTIVE To set up the HPLC fingerprints of different samples of processed Rhizoma Coptidi (RC) in order to offer evidence for identifying different processed RC and preliminary discussion on processing mechanism. METHODS Seven different samples of processed RC were determined by HPLC and the results were analyzed by Hierarchical clustering and similarity evaluation system for chromatographic fingerprint of TCM. RESULTS The characteristic of common peaks for fingerprints of different samples of processed RC is distinct, but there are differences among various processed RC. The different samples of processed RC were classified into two and the result of hierarchical clustering is correlated with the property of traditional Chinese drug. CONCLUSIONS It is proved that the method which is convenient, rapid and repeat well can be used to identify different samples of processed RC. The change of property of different processed RC is related with processing adjuvant, the possible mechanism is that new components are produced or the contents of known components have changed due to the adjuvant during processing.