Simple, convenient, sensitive and accurate analytical methods are needed for the structural characterization and identification of alkaloid components in Rhizoma Coptidis in traditional Chinese herbal medicine, which has important bioactivity. In this work, the identification of alkaloid compounds in Rhizoma Coptidis was investigated by obtaining molecular mass information using electrospray ionization mass spectrometry (ESI-MS). Multi-stage tandem mass spectrometric (ESI-MS(n)) data for the alkaloid compounds were used for detailed structural characterization, then structure information was obtained by comparison of the fragmentation mechanisms of both alkaloids in Rhizoma Coptidis and standard samples of berberine, palmatine, coptisine and jatrorrhizine by MS. Based on the results obtained, the structure of a novel compound was elucidated. The results of the experiments demonstrate that ESI-MS(n) is a sensitive, selective and effective tool for the rapid determination of alkaloids in Rhizoma Coptidis. CI - Copyright (c) 2004 John Wiley & Sons, Ltd