US Environmental Protection Agency Methods 1622 and 1623 are used for the detection of waterborne Cryptosporidium. These methods consist of filtration, elution, purification by immunomagnetic separation (IMS), and microscopic analysis for oocysts stained by a fluorescent monoclonal antibody and counter stained with 4',6-diamidino-2-phenyl indole (DAPI). DAPI counter staining is used to confirm oocysts and reduce the number of false positives. This study compared the IMS acid dissociation with heat with heat only dissociation of the parasite from the immunomagnetic beads. The effect of this change was evaluated by analyzing 48 reagent and river water samples. The average oocyst recovery in these samples improved from 28% with acid dissociation to 63% with heat only dissociation. The average DAPI confirmation rate improved from 48% to 85%. Includes 10 references, figures.