Investigation of shellfish for Cryptosporidium oocysts and Giardia cysts is of public health interest because shellfish may concentrate these pathogens in their bodies, and because shellfish are frequently eaten raw or lightly cooked. To date, the methods used for the analysis of shellfish for these parasites are based on those originally designed for water concentrates or fecal samples; the reported recovery efficiencies are frequently relatively low and the amount of sample examined is small. Here, we describe the development and use of a pepsin digestion method for analyzing shellfish samples for these parasites. The conditions of the isolation method did not affect subsequent parasite detection by immunofluorescent antibody test, and allowed examination of 3-g samples of shellfish homogenate, with recovery efficiencies from blue mussel homogenates of between 70 and 80%, and similar recoveries from horse mussel and oyster homogenates. Although exposure of the parasites to the conditions used in the technique affected their viability, as assessed by vital dyes, the maximum reduction in viability after 1-h incubation in digestion solution was 20%. In a preliminary survey of shellfish collected from the Norwegian coast, Cryptosporidium oocysts were detected in blue mussel homogenates in 6 (43%) of 14 batches and Giardia cysts in 7 (50%) of these batches. However, this relatively high occurrence, compared with other surveys, may be due to the higher recovery efficiency of the new method, and the relatively large sample size analyzed. A more comprehensive study of the occurrence of these parasites in shellfish would be of pertinence to the Norwegian shellfish industry.