Non-radioactive probes that can detect specifically North American and European isolates of porcine reproductive and respiratory syndrome virus (PRRSV) in formalin-fixed paraffin-embedded tissues by in situ hybridization were developed. These probes allow the differentiation between North American and European genotypes of the PRRS virus as well as the detection of both genotypes. Two amplified cDNA products generated by polymerase chain reaction (PCR), one from the cDNA of the Canadian PRRSV LHVA-93-3 isolate and the second one from the European Lelystad isolate, and labelled with digoxigenin were utilized as probes. The LHVA-93-3 derived probe was found to detect Canadian and USA PRRSV isolates in infected cells, while the Lelystad derived probe hybridized only with European isolates. The specificity of both probes was also demonstrated on formalin-fixed tissues collected from PRRSV infected pigs. Furthermore, by combining the LHVA-93-3 (North American) probe and the Lelystad (European) probe, successful detection of both PRRSV genotypes in fixed tissues could be achieved.