A polymethacrylate-based monolithic column was prepared and its application to the separation of three kinds of similar microcystins (MCs) in capillary high performance liquid chromatography (capillary-HPLC) with ultraviolet detection was studied. The monolithic matrix contains both hydrophobic and cation-exchange interaction sites. Factors influencing the separation performance have been investigated. A baseline separation could be achieved by means of Tris(hydroxymethyl)aminomethane buffer of mildly alkaline pH and acetonitrile as the mobile phases in less than 5 min. The calibration curves were linear with a correlation coefficient r>0.9990 over a range of 0.25-18.00 mg/L. This method was successfully applied to the separation of microcystins from other compounds in spiked uncontaminated lake water after performing solid-phase extraction. The whole procedure provided low LODs, e. g. the LODs for MC-LR, MC-YR, and MC-RR were found to be 0.49, 0.67, 0.30 microg/L, respectively. The LODs, precision, efficiency, and the results obtained for the real samples demonstrate the potential of polymethacrylate-based monolithic columns as fast separation tools for routine use in the monitoring of microcystins in real water samples.