As Microcystis cell breakage may decrease the water quality, the accurate evaluation of cell breakage is of concern in drinking water production. Well-known cell breakage indicators such as dissolved organic carbon (DOC) release and potassium release were investigated in comparison with flow cytometry coupled with a fluorescence probe. DOC release, potassium release and ratios of SYTOX Green positive cells (ruptured cells) were calibrated using known degrees of cell breakage (mixtures of live and heated cells). Good linear relationships were observed between the indicators and the known ratios of ruptured cells, with R-2 values larger than 0.925. Flow cytometry coupled with a fluorescence probe had the best overall performance, followed by potassium release and then DOC release. Moreover, the influence of factors such as extracellular organic matter (EOM), cell intake, sample conservation and strong oxidants was also studied. EOM and strong oxidants caused the overestimation and underestimation, respectively, of the cell breakage by DOC release. Potassium release had a more extensive application scope than DOC release and was only influenced by intake by residual live cells. Flow cytometry was generally not affected by EOM, cell intake or strong oxidants except during long-term storage. (C) 2015 Elsevier B.V. All rights reserved.