Chinese medicine preparations contaminated with coptisine, berberine and palmatine were studied by capillary electrophoresis-electrospray ion trap mass spectrometry. The dubious adulterants were identified by their retention times, molecular ions and specific fragment ions produced from collision induced dissociation. The results showed that, in comparison with CE-UV and capillary electrophoresis-electrospray mass spectrometry (CE-ESI-MS), more reliable identification could by achieved with CE-ESI-MS-MS using ion trap mass spectrometry.