The consumption of oysters and cockles, which are usually eaten raw or lightly-cooked, can cause outbreaks of human diseases, especially if these shellfish are harvested from polluted areas. In Brazil data about the occurrence of pathogens, like hepatitis A virus, in shellfish have been reported but research on natural contamination for pathogenic protozoa is still non-existent. Cryptosporidium oocyst contamination of oysters (Crassostrea rhizophorae) and cockles (Tivela mactroides) was evaluated during two different periods in a coastal area from São Paulo, Brazil. From June to November 2005, and from July to December 2006, 180 mollusks were harvested for tissue examination. The gills and gastrointestinal tract (n = 36 pools) were carefully extracted from the animals and homogenized in a tissue homogenizer by adding surfactant Tween 80 (0.1%). Immunofluorescence assays were performed and Cryptosporidium oocysts were detected in 50.0% of gill pools of cockles and 10.0% of gill pools of oysters. In order to evaluate seawater quality in shellfish growing areas, total levels of thermotolerant coliforms, Escherichia coli and enterococci were determined. This is the first time that Cryptosporidium oocysts were found in shellfish from the coastal region of Brazil, and to the best of our knowledge it is also the first report in Latin America and the case might be of public health importance, reflecting the extension of the contamination on seafood, requiring a need for quality control standards.