Aims: The aim of this study was to develop a method based on immunomagnetic capture and polymerase chain reaction (IC-PCR assay) for detection of Cryptosporidium parvum and Giardia intestinalis in sewage sludge. Methods and Results: The detection limit of the IC-PCR assay for both organisms was 625 oocysts and cysts ml(-1). By hybridization of PCR products the sensitivity could be increased to 125 oocysts and cysts ml(-1). Forty-four sludge samples from 12 wastewater treatment plants were examined. The samples positive for Giardia (9 out of 44) were from eight wastewater plants and the C. parvum genotype 2 samples (3 out of 44) originated from different sewage works. Conclusions, Significance and Impact of the Study: IC-PCR offers the possibility to distinguish between Cryptosporidium and Giardia genotypes. This assay can be used to monitor the presence of these organisms in a community and to determine contamination of sludge used as soil amendment.