Microcystins, which have their origin in species of cyanobacteria present in freshwaters, have recently been found to be important contaminants of the aquatic environment at trace levels. HPLC and HPCE with UV detection have been applied in the determination of such toxic compounds. Immunoaffinity chromatography for the selective extraction and clean-up of microcystins has been successfully applied to different matrices. Simple protocols for unambiguous determination of these toxins are presented and the immunoaffinity clean-up is compared with conventionally used solid phase extraction procedures. The development and optimisation of an on-line preconcentration procedure based on field amplified sample stacking for the analysis of microcystins by HPCE in the micellar electrokinetic chromatography mode is also described, using borate buffer with the anionic surfactant SDS, as separation electrolyte. Results indicate that sub-nanogram/gram content of microcystins can be detected in water samples, while sub-microgram/gram concentrations can be determined in algae samples.