Aims: The aim of this study was to compare the efficiency of peracetic acid with that of chlorine dioxide in the disinfection of wastewater from a sewage treatment plant (serving about 650 000 inhabitants) that has been using peracetic acid as a disinfectant since 1998. Methods and Results: A total of 23 samplings were made, each consisting of three samples: from secondary effluent, effluent disinfected with 2 mg l−1 of peracetic acid and effluent disinfected with 2·2 mg l−1 of chlorine dioxide (contact time 20 min). For each sample, measurements were made of the heterotrophic plate count at 36°C, total and faecal coliforms, Escherichia coli, enterococci, pH, suspended solids and chemical oxygen demand (COD). During the first phase of the experiment the peracetic acid was seen to be less efficient than chlorine dioxide. To improve the disinfectant action a system of mechanical agitation was added which led to a greater efficiency in the inactivation of bacteria of faecal origin. Conclusions: Both products were found to be influenced by the level of microbial contamination, the amount of suspended solids and COD but not by the pH of the effluent before disinfection. The immediate mixing of the wastewater and disinfectant caused a greater reduction in enterococci. Significance and Impact of the Study: Since peracetic acid was seen to produce a high abatement of micro‐organisms, it can be considered as a valid alternative to chlorine dioxide in the disinfection of wastewaters.