To our knowledge, this is the first report to demonstrate a clear difference in virulence between two well-characterized PCV2 isolates in a controlled experimental setting using a SPF pig model typical of modern pork production in North America. Since only a few genetic differences were found between the two isolates compared in this study, these two isolates and the identified genetic difference could serve as a launching pad for experimentally determining which genetic differences are important for virulence differences in the future. The availability of infectious PCV2 DNA clones and a well-defined pig model will position scientists now to further understand the molecular basis of pathogenesis of PCV2-associated diseases, develop effective vaccines, and improve diagnostic assays.