Due to eutrophication processes in our water bodies, cyanobacterial blooms can develop worldwide. Most of these blooms are toxic. The most prominent cyanobacterial toxins are the group of the microcystins, which are cyclic heptapeptides, currently with more than 100 congeners known. The biotransformation of microcystins starts with the conjugation to the cell internal tripeptide glutathione, catalysed by glutathione S-transferase enzymes. This conjugate is further broken down to a cysteine conjugate, enhancing the cell internal transport and excretion of the conjugated toxin from the organisms. Still many questions remain open, thinking on an obviously good working detoxification system on the one side and the often seen negative effects up to the death of humans on the other sides.