Abstract The need for a rapid, sensitive and reliable analytical method for cyanobacterial toxins, microcystins, has been emphasized by the awareness of toxic cyanobacteria as a human-health risk through drinking water. A new high-performance liquid chromatographic method with column switching was developed for the determination of microcystin-LR, -RR and -YR from water samples without pre-purification. The filtered water sample was passed through a Zorbax CN precolumn at a flow-rate of 3 ml/min for on-line trace enrichment. After valve switching, concentrated analytes were eluted in back-flush mode and separated on a Luna C 18 column with a gradient of acetonitrile –20 m M phosphate buffer (pH 2.5). The method showed excellent precision, accuracy and speed with detection limits of 0.02 μg/ml from 100 ml of surface water. The total analysis time per sample was about 90 min. This method improves reliability, sensitivity and sample throughput, and shortens the analysis time compared to analysis methods using off-line solid-phase extraction.