The pathogenic protozoa Giardia and Cryptosporidium have been included by the World Health Organization (WHO) among the emergent pathogenic microorganisms of prior interest, because of the numerous waterborne outbreaks of giardiasis and cryptosporidiosis that have occurred all over the world. Some rules about drinking water already include them among the regulated parameters, while in the field of wastewater reuse the problem of the presence of protozoan cysts has been considered only recently. This paper presents the results of an experimental study, carried out at Pistoia's Waste Water Treatment Plant (WWTP), aimed at determining the presence of such protozoa in raw wastewater and at estimating and comparing the removal achievable by a conventional WWTP and by a pilot plant scale tertiary treatment which consists of a double stage filtration. According to the literature data, experimental results show that the average values of Giardia cysts and Cryptosporidium oocysts removal obtained by a conventional WWTP are about 98% and 92%, respectively. Also, it was determined that physical removal through filtration is a treatment suitable and reliable for an effective elimination of cysts and oocysts in wastewater. By filtering the secondary effluent an average removal value of 98% for Giardia cysts and 90% for Cryptosporidium oocysts has been obtained. Includes 13 references, tables, figures.