The protozoan parasite Cryptosporidium has emerged as one of the most important contaminants of water, causing waterborne outbreaks of gastroenteritis worldwide. To monitor and understand the public health significance of this pathogen in environmental samples, several methods have been developed to isolate and detect Cryptosporidium oocysts. The purpose of this study was to perform the first investigation on the presence of Cryptosporidium spp. oocysts in raw sewage and creek water in the city of São Paulo, Brazil. The oocysts were concentrated by flocculation and membrane filtration. The results showed the occurrence of Cryptosporidium spp. in all wastewater samples analyzed, indicating a possible risk for dissemination of these pathogens in aquatic environment and in the community.