The intestinal parasites Cryptosporidium and Giardia cause gastro-enteritis in humans and can be transmitted via contaminated water. Oysters are filter feeders that have been demonstrated to accumulate pathogens such as Salmonella, Vibrio, norovirus and Cryptosporidium from contaminated water and cause foodborne infections. Oysters are economically important shellfish that are generally consumed raw. Commercial and non-commercial oysters (Crassostrea gigas) and oyster culture water from the Oosterschelde, The Netherlands, were examined for the presence of Cryptosporidium oocysts and Giardia cysts. Nine of 133 (6.7%) oysters from two non-commercial harvesting sites contained Cryptosporidium, Giardia or both. Six of 46 (13.0%) commercial oysters harboured Cryptosporidium or Giardia in their intestines. Data on the viability of (oo)cysts recovered from Oosterschelde oysters were not obtained, however viable (oo)cysts were detected in surface waters that enter the Oosterschelde oyster harvesting areas. The detection of Cryptosporidium and Giardia in oysters destined for human consumption has implications for public health only when human pathogenic (oo)cysts that have preserved infectivity during their stay in a marine environment are present. Our data suggest that consumption of raw oysters from the Oosterschelde may occasionally lead to cases of gastro-intestinal illness.