Three capillary electrophoresis methods, using UV detection, were developed for the simultaneous determination of several tropane alkaloids, including atropine, scopolamine and synthetic derivatives. After optimization, the validated capillary zone electrophoresis methods were applied to the determination of these compounds in various pharmaceutical forms, such as ophthalmic and injection solutions, tablets, suppositories and aerosols. Capillary electrophoresis in the micellar mode was found to be more appropriate for the analysis of hyoscyamine and scopolamine in plant material. These two compounds are generally found together with other tropane alkaloids which present similar structures and charge to mass ratio. Furthermore, the separation of positional isomers, such as hyoscyamine and littorine generally encountered in plant extracts, was also considered. The developed method was applied to the analysis of hairy root extracts of Datura candida x Datura aurea, Datura quercifolia and Hyoscyamus albus.