Peracetic acid and hypochlorite were compared as disinfectants, with a focus on the disinfection of particulate-containing combined sewer overflows (CSOs). Hypochlorite is widely used to disinfect water and wastewater, although its use for disinfection of CSO discharges raises concerns regarding safety and efficiency. Peracetic acid (PAA) is an alternative that may be more environmentally-friendly and cost-effective for CSOs. Inactivation experiments were conducted on suspended cultures of Escherichia coli and wastewater SS. While efficiency of disinfection by hypochlorite decreased with increasing solids size, particle size had no appreciable effect on PAA disinfection. It was also found that, while higher pH values significantly decreased PAA disinfection efficiency, the efficiency of hypochlorite was unchanged. Fluorescence microscopy coupled with plating revealed that disinfection of wastewater samples by PAA leaves cells viable, but not culturable. Investigation into the mechanics of disinfection by PAA and hypochlorite was attempted via Fourier Transform Infrared Spectroscopy (FTIR). Preliminary results did not show a significant difference in the affected functional groups.