This paper presents a simple and rapid screening method for Cryptosporidium parvum, using molecular techniques in a multi-well microplate format. The currently recommended method for C. parvum detection in drinking water cross-reacts with other Cryptosporidium species, has a low recovery efficiency, and is costly and time-consuming. In addition, the drinking water industry still lacks simple, rapid methods for general pathogen detection and identification that are easily amenable to automation. To overcome these problems, a rapid, semi-automated method is being developed that involves nucleic acid labeling during amplification by polymerase chain reaction (PCR). The amplicons are captured in microplates by liquid hybridization to a pre-attached specific probe. The amplicon-probe hybrids are detected by an enzymatic colorimetric reaction. The formation of a purple/brown precipitate within the microplate wells indicates the presence of C. parvum, whereas negative samples remain clear.