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In Italy, urban wastewater disinfection is regulated in the third part of Legislative Decree n. 152/2006, which states that wastewater treatment plants (WWTPs) must include a disinfection unit, with a capacity exceeding 2000 Population Equivalent (PE). This treatment shall ensure microbial quality and health security. The legislation provides the following limits for wastewater: Escherichia coli (E. coli) concentration below 5000 CFU 100 mL−1 (recommended value), active chlorine concentration below 0.2 mg L−1 and lack of acute toxicity. The compliance with these conditions is shown by means of the study of correct disinfectant dosage, which also depends on wastewater characteristics. An investigation at the regional level (from 2013 to 2016) shows a correlation between acute toxicity discharge and disinfection treatment through chemical reagents (mainly with the use of chlorine compounds and peracetic acid). The experimental work concerns two active sludge WWTPs in northern Italy with small capacity (10,000–12,000 PE). The activities provide the assessment of microbiological quality and toxicity of WWTPs effluents in relation to the dosage of sodium hypochlorite and peracetic acid, by means of the use of batch tests. The results show that with similar disinfectant dosage and comparable initial E. coli concentration, peracetic acid exhibits the best performance in terms of microbial removal (with removal yields up to 99.99%). Moreover, the acute toxicity was evident at higher doses and therefore with higher residuals of peracetic acid (2.68 mg L−1) compared to the free residual chlorine (0.17 mg L−1).