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Waterborne pathogens are of great concern in public drinking water. Outbreaks of Cryptosporidiosis have resulted in a heightened awareness of the need to routinely screen our drinking water supplies. The current test for Cryptosporidium requires fluorescent labeled antibodies in an immunofluorescent assay. This assay is time consuming, requires trained personnel and results in poor recoveries. This paper describes a new assay to rapidly and reproducibly test multiple water samples for Cryptosporidium using a nucleic acid amplification system. The assay procedure includes the isolation of total nucleic acid by repeated freezing and thawing to break open the hard-shelled oocysts. The method has been shown to be extremely sensitive (down to 1 oocyst) and can be semi-quantitative when compared to a standard titration with a known number of Cryptosporidium oocysts.