Several disinfection processes of ultraviolet (UV), chlorine or UV followed by chlorine were investigated in municipal wastewater according to the inactivation of Escherichia coli, Shigella dysenteriae and toxicity formation. The UV inactivation of the tested pathogenic bacteria was not affected by the quality of water. It was found that the inactivated bacteria were obviously reactivated after one day in dark. Fluorescent light irradiation increased the bacteria repair. The increase of UV dosage could cause more damage to bacteria to inhibit bacteria self-repair. No photoreactivation was detected when the UV dose was up to 80 mJ/cm2 for E. coli DH5alpha, and 23 mJ/cm2 for S. dysenteriae. Nevertheless, sequential use of 8 mJ/cm2 of UV and low concentration of chlorine (1.5 mg/L) could effectively inhibit the photoreactivation and inactivate E. coli below the detection limits within seven days. Compared to chlorination alone, the sequential disinfection decreased the genotoxicity of treated wastewater, especially for the sample with high NH3-N concentration.