A method for enzyme-based in situ hybridisation of Streptococcus suis was developed. It enables the light microscopic localization of bacterial ribosomal RNA (rRNA) in formalin-fixed paraffin-embedded tissues. A unique sequence in the 16S rRNA of S. suis was targeted. Different pretreatment protocols were applied to facilitate probe penetration and multiple detection systems were tested. The results were compared to those obtained by immunohistochemistry. Pretreatment was necessary to obtain a signal by in situ hybridisation. The use of proteinase-K pretreatment was optimal regarding sensitivity and preservation of tissue morphology. A strong specific in situ hybridisation signal was achieved in tissue sections containing S. suis in microcolonies and the microanatomy of the surrounding tissue was easily assessed. However, the signal distribution differed from that found immunohistochemically and low-grade infection could not be detected by in situ hybridisation. These findings were interpreted as reflecting the physiological state of the bacteria. Thus, this method could prove useful in future studies of the infection pathogenesis.