Porcine circovirus 3 (PCV-3) has been detected in diseased and healthy pigs of different ages. Several reports have associated the agent with reproductive failure and mummified and stillborn piglets. One report from North America has proposed a consistent potential association with postweaning disorders. Thus, the present case report aimed to describe the histopathological lesions and their association with the presence of PCV-3 genome in postweaning pigs showing growth-retardation and thrown-back ears. All affected animals displayed multi-organic lymphoplasmacytic periarteritis, lymphocytic myocarditis and/or lymphoplasmacytic meningoencephalitis. PCV-3 genetic material was detected by in situ hybridization within the lesions and confirmed by PCV-3 real-time quantitative PCR detection in tissues. This study represents the first report of PCV-3 associated with clinical disease in postweaning pigs in Europe.