We have developed a unique qPCR system for performing a panel of diagnostic tests, up to FIVE-plex (depending on the qPCR platform used). As well as having the sensitivity and specificity required for diagnostic pathogen detection, this system also incorporates flexibility, allowing the laboratory to pick and choose the pathogens of interest. The system incorporates an internal extraction/PCR inhibition control, plus one or more targets of choice, up to a maximum of four (one internal control plus four pathogen targets). The flexibility and specificity of this system is achieved by incorporating MNAzyme probe technology. A unique feature of the MNAzyme technology is having separate target and probe sensing domains which give it superior multiplexing capabilities. MNAzyme qPCR has 4 levels of specificity requiring primers to bind and extend to generate the amplicon for the MNAzyme components to bind cleaving the universal probe, thus generating a fluorescent signal. A series of universal probes have been developed that are highly specific and compatible for multiplexing and can be matched with most targets. The sensitivity, specificity and robustness of the assay is further enhanced by use of the proprietary buffer chemistry, SensiFAST™ Probe Kit, which has been optimized over a wide dynamic range of target concentrations. Together, the unique probe technology and optimized qPCR reagent, provides exceptional specificity and sensitivity in either single or multiplex assays. The prototype for this system was built using an enteric panel of assays, targeting up to four enteric pathogens and one internal control as multiplex or duplex assays (a single target plus control). Furthermore, this system can also be applied to other panels of pathogens.