Microcystins are an increasingly important group of bioactive compounds produced by a number of mainly planktonic cyanobacteria. They are a family of cyclic heptapeptides that cause both acute and chronic toxicity. Purified microcystins are utilised in a range of research applications including toxicological and biochemical studies, development of detection systems and the investigation of water treatment strategies. The commercial availability of purified microcystins is still relatively limited and for many projects the cost of their purchase prohibitive. The purification of microcystins from both bloom material and laboratory cultures is reviewed including a discussion on extraction, separation, and the determination of purity and yield.