Background: Numerous multiplex-PCR assays are now available in routine diagnostics but their clinical value is controversial if a clear association between clinical symptoms and the detection of a particular pathogen is missing. The objective of this work was to evaluate a multiplex-PCR assay for the diagnosis of traveller’s diarrhoea (TD) in a case-control study and to assess the concordance with the BioFire® FilmArray® Gastrointestinal Panel. Methods: Stool samples from cases (n = 61) and controls (n = 30) were collected during travel and analysed by the GI-EB Screening assay (Seegene) in a case-control study. The concordance with the BioFire® FilmArray® Gastrointestinal Panel was expressed as the proportion of participants in which both tests agreed in the category "detected" and "not detected". Results: None of the test-target organisms ('Campylobacter' spp., 'Clostridioides difficile' toxin A/B, 'Salmonella' spp., 'Shigella' spp./enteroinvasive 'Escherichia coli', 'E. coli' O157, Shiga toxin-producing 'E. coli', 'Yersinia enterocolitica') was significantly associated with TD GI-EB Screening assay. The GI-EB Screening assay had an agreement with the BioFire® FilmArray® of 86.8–100%. Conclusion: The selection of test-target organisms included in the GI-EB Screening assay appears inappropriate for the diagnostic work-up of TD as none of the detected pathogens was associated with TD. The GI-EB Screening assay had a good concordance with BioFire® FilmArray®.