This paper discusses a polymerase chain reaction (PCR) based detection method that was adapted to a relatively simple, semi-automated, 96 well microplate format to provide rapid detection of waterborne C. parvum with high sample throughput. C. parvum-specific amplicons were captured by a biotin-labeled probe pre-attached to streptavidin coated microplate wells. The immobilized amplicon-probe hybrids were detected by an alkaline phosphatase mediated colorimetric reaction. The intensity of the color reaction was proportional to the number of oocysts. This approach eliminated the subjective identification of positive samples which is a major limitation of the current microscope-based immunofluorescent assay method. Another major advantage of this technique is that it has the potential to analyze up to 384 samples simultaneously without greatly increasing the processing time. Includes 8 references, figures.