Porcine circovirus type 2 (PCV2) has been present for the last 2 decades in Croatia, with its highest incidence level in 2004. The clinical features of the disease have altered within this period. Infections until 2008 were mostly accompanied by severe signs such as enteritic and respiratory disorders, erythematous skin lesions that showed a tendency to progress to dermal necrosis accompanied by a high mortality rate of primarily 4 to 16 week-old pigs. Later PCV2 infections were milder and mostly manifested as waste loss and poor growth performance as well as reproductive failure in pregnant sows. In both cases the disease had a direct negative impact on the pig production. Since the infection is continuously present in some regions of Croatia, the heterogeneity of detected PCV2 strains prior to 2008 with strains isolated in 2012 were compared for a better insight in the epidemiological situation. The results of phylogenetic analysis revealed that the viral strains found in 2012 genetically differ from those detected in earlier years. This indicates that new entries into the pig population appeared probably due to pig trade.