Micellar electrokinetic capillary chromatography was applied to the simultaneous analysis of six tropane alkaloids, including hyoscyamine and scopolamine. Successful results were obtained using a 30 mM boratephosphate buffer at basic pH (8.5) in the presence of 50 mM sodium dodecyl sulfate. The operating conditions, such as buffer concentration and pH, micelle concentration and organic modifier type and percentage were also discussed on the basis of the results given with a tropane alkaloid mixture. Addition of organic modifiers showed an improvement in separation efficiency and resolution. Moreover, hyoscyamine and littorine, two positional isomers, were only resolved by the addition of organic solvents such as methanol or acetonitrile. The optimized conditions were finally applied to the analysis of tropane alkaloids found in genetically transformed root cultures ofDatura candida x D. aurea.