The results reported in this communication demonstrate that capillary zone electrophoresis (CZE) can be used easily for the quantitative determination of the potential anticancer drugs berberine and isoguanosine in the extract of the traditional Chinese medicinal herb. Isoguanosine and berberine can be monitored selectively and sensitively at 254 nm within 14 min in the plant extract using a 100-mM sodium citrate running buffer (adjusted to pH 2.7; applied voltage 12 kV). The concentration range of 0.1-50 micrograms ml-1 proved to be sufficient for exact quantification and the peak profile showed good reproducibility [relative standard deviations (n = 32); for the migration time 0.22% (isoguanosine) and 1.32% (berberine); for the peak area 2.8% (isoguanosine) and 3.2% (berberine)]. The measured concentrations in the crude extract were 1.3 micrograms ml-1 for isoguanosine and 8.7 micrograms ml-1 for berberine. In addition to the better separation performance, CZE shows several other remarkable advantages over high-performance liquid chromatography (HPLC), such as rapidity of analysis, small sample volume, no requirement of organic solvent in the running buffer and low cost of reagents.