In this work, the efficiency and the applicability of some disinfection systems for biologically treated wastewater were studied. The following disinfection processes were considered: peracetic acid (PAA), chlorine dioxide, ozone, UV light. These treatments were chosen as an alternative to chlorination. Their applicability was investigated considering both the removal efficiency of microorganisms and the qualitative changes in the treated effluent (e.g. presence of disinfectant residues, disinfection by-products, etc.). The different processes were tested by means of pilot scale plants working in parallel; in fact they were fed with the same wastewater (secondary effluent of a municipal wastewater treatment plant). Finally, an economical analysis was carried out.