AIM: The sensitive detection of pathogenic Yersinia enterocolitica in paraffin embedded tissue sections by in situ hybridisation (ISH). METHODS: Y enterocolitica infected cell lines, rat spleens, and patient biopsy specimens were used to compare conventional ISH, immune fluorescence assay (IFA) detection, and catalysed reporter deposition (CARD) signal amplification ISH. RESULTS: CARD-ISH was shown to be more sensitive then conventional ISH and had a comparable sensitivity to IFA. In contrast to IFA, CARD-ISH preserved good tissue morphology. CONCLUSIONS: CARD-ISH appeared to be a fast and sensitive ISH method for detecting Y enterocolitica in routinely processed tissue sections. Application of this method allows the combination of routine detection and cellular localisation of the pathogen within the infected tissue.