Microcystins are cyclic peptide hepatotoxins that are produced during blooming of cyanobacteria. In recent two decades they gained a great interest because of the related ecological and public health risks. Over 70 different analogs of microcystins have been isolated from natural blooms and laboratory cultures of cyanobacteria. Because they are inhibitors of protein phosphatases they act as tumor promoters, but on the other hand, inhibitive enzymatic and ELISA methods may be employed for their screening or quantitative determination. Much larger analytical potential for this purpose have, however high-performance separation chromatographic and electromigration techniques. Based on about 70 references from original journal papers these methods are reviewed together with presentation of their preconcentration methods and clean-up procedures for analyzing environmental samples. Some attention is also focused on increasing application of LC/MS methods, and comparison of separation techniques with immunochemical or enzymatic methods.