A non-radioactive in situ hybridization (ISH) method developed recently and an immunohistochemical method, the immunogold silver staining (IGSS), were compared for the detection of porcine reproductive and respiratory syndrome virus (PRRSV) in formalin-fixed paraffin-embedded tissues. Serial sections from 98 tissues, representing different organs from PRRSV experimentally infected pigs, and serial sections from 46 lung tissues from field cases were tested by both methods. Results obtained on tissues from experimentally infected pigs and tissues from field cases demonstrated that ISH was more sensitive than immunohistochemistry. More tissues were positive by ISH compared to IGSS and also a greater number of labelled cells and a stronger signal in stained cells were observed in ISH-treated sections. The ISH method described, using a 254 bp digoxigenin-labelled cDNA probe, is a rapid, highly specific and sensitive detection method which can be used for the diagnosis of PRRSV in routinely fixed and processed tissues.