The technique of capillary electrophoresis - mass spectrometry (CE-MS) was applied for determination of isoquinoline alkaloids in crude methanolic extracts of medicinal plants. For the CE separations ammonium formate buffer solutions (70 or 100 mM, pH 3.0 or 4.0) containing 10% methanol or 20-60% acetonitrile as additives were used. The applied voltage was 25 kV, the thermostating temperature was kept constant at 25 degrees C. Coupling with the mass spectrometer was performed via an atmospherical pressure ionization (API) interface and the electrospray ionization technique (ESI). As sheath liquid 5 mM formic acid in acetonitrile at a flow rate of 3 microL/min was used. The spray voltage was 4.5 kV and the temperature of the heated capillary was chosen to be 200 degrees C. Detection in the positive ionization mode resulted in mass spectra showing either the molecular ions [M]+ or the protonated molecular ions [M+H]+. The presented method allows detection and identification of isoquinoline alkaloids in crude methanolic extracts of medicinal plants as Eschscholzia californica CHAM. (Papaveraceae), Hydrastis canadensis L. (Ranunculaceae), Berberis vulgaris L. (Berberidaceae), Jateorhiza palmata (LAM.) MIERS (Menispermaceae) and Chelidonium majus L. (Papaveraceae).