We describe a capillary zone electrophoresis method coupled to electrospray ionization (ion trap) mass spectrometry (CZE-ESI-MS) for the identification and determination of choline and atropine compounds in hairy root extracts from Cannabis sativa L. Fused-silica capillary and an alkaline solution of 20 mM ammonium acetate at pH 8.5 are used being the most suitable for the analysis of choline and atropine in less than 10 min. Under the optimized conditions, including CE and ESI-MS parameters, the method resolved both compounds with very high sensitivity. The system exhibited good linear response in the range of 25-500 mg/L and 500-1000 microg/L for choline and atropine, respectively. The detection limit of choline was 18 mg/L and 320 microg/L for atropine. Finally, the developed method was applied to the analysis of these compounds in transgenic root cultures of Cannabis sativa L.