Drinking water disinfection by chlorine is known to reduce concentration of microcystin, but compounds formed are rarely considered. In this work the chlorination of microcystin-LR has been studied by monitoring reactants consumption and reaction products using the linear trap quad-Orbitrap (LTQ-Orbitrap) technology. Microcystin-LR was totally transformed within 2 min, meanwhile chlorine was consumed until 30 min with a rate of 12 mol per mol of toxin. Four new by-products of microcystin-LR were identified as well as their isomers: monochloro-microcystin, monochloro-dihydroxy-microcystin, dichloro-dihydroxy-microcystin and trichloro-hydroxy-microcystin. In addition, four new isomers were also observed, corresponding to the dihydroxy-microcystin already known. Besides, another compound previously observed was identified as monochloro-hydroxy-microcystin.