Inactivation of Microcystis aeruginosa by UV/chlorine process was investigated in this study. Chlorine decay with or without the presence of algal cells was modeled based on a kinetic model, and the second-order rate constant between chlorine and algal cells was determined to be 3.3 x 10(-4) (mgC/L)(-1) s(-1). Flow cytometry as well as confocal laser scanning microscopy were used to characterize the cell integrity of M. aeruginosa. Results demonstrated that UV/chlorine pre-oxidation was responsible for the inactivation of M. aeruginosa, and the inactivation efficiency increased with the increasing dosage of chlorine. UV/chlorine process can significantly change the surface characteristics of M. aeruginosa and enhance the coagulation efficiency. Moreover, due to the destruction of algal cells, microcystin-LR would be released and then degraded during pre-oxidation, and the releasing endotoxin could be removed during subsequent coagulation-sedimentation process. This study suggests that UV/chlorine process might be a potential alternative for the pretreatment of cyanobacterial cells in treating cyanobacteria-laden water.