Detection and enumeration of Cryptosporidium parvum in both treated and untreated waters are important to facilitate prevention of future cryptosporidiosis incidents. Immunomagnetic separation (IMS)-fluorescent antibody (FA) detection and IMS-PCR detection efficiencies were evaluated in two natural waters seeded with nominal seed doses of 5, 10, and 15 oocysts. IMS-FA detected oocysts at concentrations at or below the three nominal oocyst seed doses, illustrating that IMS-FA is sensitive enough to detect low oocyst numbers. However, the species of the oocysts could not be determined with this technique. IMS-PCR, targeting the 18S rRNA gene in this study, yielded positive amplification for 17 of the 18 seeded water samples, and the amplicons were subjected to restriction fragment length polymorphism digestion and DNA sequencing for species identification. Interestingly, the two unseeded, natural water samples were also PCR positive; one amplicon was the same base pair size as the C. parvum amplicon, and the other amplicon was larger. These two amplified products were determined to be derived from DNA of Cryptosporidium muris and a dinoflagellate. These IMS-PCR results illustrate that (i) IMS-PCR is able to detect low oocyst numbers in natural waters, (ii) PCR amplification alone is not confirmatory for detection of target DNA when environmental samples are used, (ii) PCR primers, especially those designed against the rRNA gene region, need to be evaluated for specificity with organisms closely related to the target organism, and (iv) environmental amplicons should be subjected to appropriate species-specific confirmatory techniques.Cryptosporidium parvum, an intestinal protozoan parasite, continues to be an important cause of waterborne gastrointestinal disease worldwide. Due to oocyst robustness consisting of environmental stability and resistance to normal water disinfection processes (14,22), the low infectious dose (10), and the lack of chemotherapy (23), detection and enumeration of this organism in both treated and untreated waters have become a focus of the water industry in order to prevent future incidents of cryptosporidiosis.The currently accepted technique for oocyst recovery from water samples is immunomagnetic separation (IMS)-fluorescent antibody (FA) detection, as described by United States Environmental Protection Agency (EPA) Method 1623 (25). The reported IMS-FA recovery rates for oocysts seeded into previously concentrated water pellets of various turbidities have been 62 to 100% (oocyst seed density as determined by dilution, 36 to 976) (20), 55.9 to 83.1% (oocyst seed density as determined by dilution, 89.1 to 98.7) (17), 68 to 83% (oocyst seed density as determined by dilution, 525 to 870) (3), and 84.3% (oocyst seed density as determined by flow cytometry, 100) (19). In an additional study, in which oocysts were seeded into 10-liter grab samples of various turbidities, the reported recoveries ranged from Ͻ1.7 to 56.6% (oocyst seed densities, 1,615 and 2,880) (8).However, the criteria for o...