Non-radioactive digoxigenin (DIG)-labelled probes that can differentiate porcine circovirus (PCV) 1 from PCV2 in formalin-fixed, paraffin-wax-embedded tissues by in-situ hybridisation were developed. A 349 base pair (bp) DNA fragment from open reading frame (ORF) 1 of PCV1 and a 481 bp DNA fragment from ORF2 of PCV2 generated by polymerase chain reaction (PCR) were used as PCV1 and PCV2 probes, respectively. A specific DIG-labelled PCV1 DNA probe did not hybridise with PCV2-infected PK-15 cells and vice versa. From the 40 field cases with postweaning multisystemic wasting syndrome tested by in-situ hybridisation, 30 (75 per cent) cases were PCV2-positive only and 10 (25 per cent) cases were positive for both PCV1 and PCV2. PCV1 and PCV2 DNAS were detected mainly in the macrophages of lymph nodes and spleens. Positive cells typically exhibited a dark brown to black reaction product mainly in the cytoplasm but also occasionally in the nucleus. In-situ hybridisation together with the differential probes developed in the present study represent an additional tool capable of differentiating of both types of PCV in formalin-fixed, paraffin-wax-embedded tissues.