Background Cause for gastroenteritis range from viral, bacterial to parasitic pathogens. Rapid Multiplexing techniques like ProGastro_SSCS and xTAG_GPP can detect broad panels of pathogens simultaneously. We performed a field test with a total number of 347 stool samples from adult hospitalized patients that were tested with the Luminex xTAG GPP assay; of the 157 samples positively tested for at least one pathogen by xTAG GPP a total number of 30 samples was retested with the ProGastro SSCS assay. Assays were compared to standard routine diagnostics. Findings Multiplexing significantly reduced the time to the initial identification of a pathogen. Moreover, multiplexing detected pathogens for which a diagnostic assays was not requested by the physician and thus may be an important tool for avoiding nosocomial outbreaks. Conclusion This first frontline approach with these assays approves their utility compared to conventional microbiological methods.