The potential of nonaqueous capillary electrophoresis has been investigated for the separation of structurally similar tropane alkaloids. The effects of the organic solvent and of electrolyte composition on separation selectivity, migration times, and efficiency are described. The addition of trifluoroacetic acid to the separation buffer was found beneficial for manipulation of the order of migration of the two positional isomers littorine and hyoscyamine. Replicate injections under nonaqueous conditions gave migration time and peak area data of excellent precision. The application of the optimized conditions to the analysis of hyoscyamine and scopolamine in genetically transformed root cultures ofDatura candida x D. aurea is presented.