Capillary zone electrophoresis, coupled to UV and interfaced with electrospray ionization mass spectrometry (ESI-MS), is described for the simultaneous analysis of hyoscyamine and scopolamine. On-line UV detection occurred at 22 cm from the inlet of the capillary and ESI-MS monitoring was performed along the entire length of the capillary (85 cm). An alkaline solution of 40 mM ammonium acetate at pH 8.5 was suitable for the analysis of the alkaloids under consideration. Under the optimized conditions, including CE and ESI-MS parameters, the two alkaloids were resolved within a short time and with very high sensitivity. The differentiation of hyoscyamine and its positional isomer littorine, commonly encountered in plant material, is also presented using up-front collision-induced dissociation. Finally, the developed method was applied to the analysis of these alkaloids in Belladonna leaf extract and in Datura candida x D. aurea hairy root extract.