A comparative study on peracetic acid and sodium hypochlorite in inactivating bacteria and viruses was carried out. Therefore the disinfection actions of peracetic acid, in comparison with sodium hypochlorite, was evaluated against the usual indicators of faecal contamination, the pathogen Salmonella, Pseudomonas spp., bacteriophages anti-Escherichia coli, F+/phage and the phage of Bactericides fragilis B40-8 and enteroviruses. Under the experimental conditions, no representative results were obtained for enteroviruses and phages because of their low concentration in the sewage effluent. On the other hand, the indicator organisms were reduced substantially by the sodium hypochlorite and peracetic acid concentrations, while more variable results were obtained against Pseudomonas and bacteriophages anti-Escherichia coli.