We investigated the possibility to apply performic acid (PFA) and peracetic acid (PAA) for disinfection of combined sewer overflow (CSO) in existing CSO management infrastructures. The disinfection power of PFA and PAA to Escherichia coli (E. coli) and enterococcus were studied in batch scale and pre-field experiment. In batch scale experiment 2.5 mg·L -1 PAA removed around 4 log unit of E. coli and enterococcus from CSO with long contact time. Removal of E. coli and enterococcus from CSO were always around or above 3 log unit using 2-4 mg·L -1 PFA with short contact time in batch scale and pre-field experiment. There were no toxicological effect measured by Vibrio fischeri when CSO was disinfected with PFA, slight toxicological effect was observed on CSO disinfected with PAA. When the design for PFA based disinfection was applied to CSO collected from an authentic event. Disinfection efficiencies were confirmed and degradation rates were slightly higher than predicted in simulated CSO.