This paper presesnts a simple and rapid screening method for Crytopsporidium parvum and enteroviruses using molecular techniques in a multi-well microplate format. The currently recommended method for C. parvum detection in drinking water cross-reacts with other Crytopsporidium species, has a low recovery efficiency, and is costly and time-consuming. Enteroviruses detection still relies on a few cell lines as hosts which possess limited sensitivity. Each cell line also exhibits different sensitivity to each enterovirus, and may support the growth of human as well as non-human enteroviruses. The cell culture method is labor intensive, costly, and results are not available for 4-6 weeks after onset of analysis. 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, an rapid, semi-automated method is being developed that involves nucleic acid labeling during amplification. The amplicon-probe hybrids are captured in a multi-well, streptavidin-coated microplate by the strong biotin-streptavidin bond. Liquid hybridization using non-radioactively labeled oligoprobes is conducted directly in the microplate. The amplicon-probe hybrids are detected by enzymatic colorimetric, fluorometric or chemiluminescent reactions. Three liquid hybridization and detection approaches have been investigated using C. parvum as target organism, and then applied to the enteroviruses. Includes 5 references, figures.