Potatoes, members of the Solanaceae plant family, contain calystegines, water-soluble nortropane alkaloids, which are biologically active as glycosidase inhibitors. The content of calystegines A(3) and B(2) in different varieties of potato and in various parts of the tubers (whole potato, peel, flesh, and sprouts) were analysed by new capillary zone electrophoresis and capillary isotachophoresis methods and by the routine GC method. The optimized background electrolyte for capillary zone electrophoretic analysis was mixture of 20 mM histidine, 20 mM N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid and 20% (v/v) methanol in demineralized water. Calystegines were detected by indirect UV detection at 210 nm. A clear separation of calystegines from other components of the methanolic sample extract was achieved within 4 min. The electrolytes for isotachophoretic analysis consisted of 5 mM NH(4)OH, 10 mM N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid, 0.1% hydroxyethylcellulose and 20% (v/v) methanol in demineralized water (leading) and 5 mM histidine+10 mM acetic acid+20% (v/v) methanol in demineralized water (terminating). Calystegines were separated within 20 min and detected by a conductimeter. Method characteristics of both zone electrophoresis and isotachophoresis, i.e., linearity (10-100 ng/microl and 1-10 ng/microl), accuracy (recovery 96+/-5% and 98+/-4%), intra-assay repeatability (4.2% and 3.5%), and detection limit (3 and 0.4 ng/microl) were evaluated. Simple sample preparation, sufficient sensitivity, speed of analysis, and low running cost are important attributes of the electrophoretic methods. The overall results of electrophoretic methods were comparable with GC.