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Flow cytometric cell sorting (FCCS), followed by microscopic verification, was evaluated as an alternative to immunofluorescence assay (IFA). Two hundred and sixty-two water samples were stained with either indirectly conjugated or directly conjugated anti-Cryptosporidium and anti-Giardia antibodies and were examined by IFA and FCCS, respectively. Relative sensitivities of each assay were calculated by dividing the number of positive samples detected by one assay by the number of positive samples detected by either assay. When samples analyzed within five months of the initial IFA analysis were compared, the relative sensitivities of FCCS for detection of Cryptosporidium and Giardia were 94.1 and 78.6 percent, respectively, whereas the relative sensitivities using the IFA were 35.3 and 61.4 percent. Identification of Cryptosporidium and Giardia in water samples using FCCS takes less time, costs less, and analyzes a greater sample volume than the IFA. Given the nearly threefold increase in relative sensitivity for Cryptosporidium detection and the equal relative sensitivities for Giardia detection, the authors support the use of FCCS for routine detection of Cryptosporidium and Giardia in environmental samples. Includes 15 references, tables, figures.