A capillary electrophoresis (CE) method using non-aqueous (NA) separation solutions combined with an ion trap mass spectrometer (MS and MS/MS) as detection device is presented for the separation, identification and quantification of isoquinoline alkaloids from Fumaria officinalis. The best results were obtained with a mixture of acetonitrile-methanol (9:1, v/v) containing 60mM ammonium acetate and 2.2M acetic acid as running electrolyte and an applied voltage of 30 kV. Electrospray MS measurements were performed in the positive ionization mode with isopropanol-water (1:1, v/v) as sheath liquid at a flow rate of 3 microl/min. Alkaloids were detected as [M+H](+)-ions and showed typical fragmentation patterns in MS/MS experiments. The developed assay was used for the quantification of seven isoquinoline alkaloids representing different structural subtypes in Fumariae herba extracts and F. herba containing phytopharmaceuticals.