In the last years, effluent from hospitals and health care institutes has obtained a raising concern in terms of management and treatment, due to the presence of different kinds of substances which could cause serious consequences to the environment, once immetted into surface water bodies. These pollutants include not only chemical reactives, heavy metals, disinfectants, sterilizants, radioactive markers, but also pharmaceuticals and their metabolites, resistant bacteria, pathogens, viruses, due to laboratory and research activities or human excretion. The management and the treatment of hospital wastewaters (WWs) are an interesting field of research and discussion for scientists, hygienists, environmental engineers, econonomists and administrators (Laber et al. 1999; Chitnis et al., 2000; Altin et al., 2003; Pauwels et al., 2006; Verlicchi et al., 2008). In many European countries, effluents from hospitals are quite often directly immetted in public sewage and conveyed to a municipal wastewater treatment plant (WWTP) where they are subjected to the same (conventional) treatments as domestic WWs. In few cases, hospital effluents have subjected to a (complete) dedicated/separated treatment or to a separated treatment and then to cotreatment at a municipal WWTP. In other countries, hospital effluents are directly discharged into a surface water body, contributing in this way to the spread of resistant bacteria in the environment. This practice is unfortunately quite common in some countries of Eastern Europe and Southern America, where, often, even a treatment for domestic WWs is not available. In these cases, an on site basic treatment can reduce the risk of dissemination of pathogens into the environment. This paper reports the results of an experimental investigation on the bacteria removal from a hospital effluent subjected to mechanical and chemical treatments in a compact system. Two different chemical agents (sodium hypochlorite NaClO and peracetic acid CH3COOOH) have been tested at different concentrations and different contact times.