Thirty-eight natural cases of aetiologically unclear non-suppurative encephalitis in pigs were studied retrospectively. Brain samples were examined for the presence of porcine circovirus type 2 (PCV-2), porcine respiratory and reproductive syndrome virus (PRRSV), porcine enteroviruses (PEVs), ovine herpesvirus type 2 (OvHV-2), Borna disease virus (BDV) and suid herpesvirus type 1 (SuHV-1) by molecular biological and immunohistochemical methods. Histological examination of the brains revealed variable degrees of lymphohistiocytic encephalitis or meningoencephalitis, characterised predominantly by perivascular mononuclear infiltrates. Two cases could be attributed to PCV-2 infection by in situ hybridisation: viral nucleic acid was found in the mesencephalon, the cerebellum and the medulla oblongata, mainly in the cytoplasm of macrophages, endothelial cells and some glial cells, which were predominantly found in the meninges and around blood vessels. Real-time PCR detected PCV-2 DNA in brain samples from seven other pigs. There was no evidence of PRRSV, BDV, SuHV-1, PEVs or OvHV-2 in any of the brain samples examined.