The ability of S. aureus to infect bone and osteoblasts is correlated to its incredible virulence armamentarium that can mediate the invasion/internalization process, cytotoxicity, membrane damage and intracellular persistence. We comparatively analyzed the interaction, persistence and modulation of expression of selected genes as well as cell viability in an ex-vivo model using human MG-63 osteoblasts of two previously studied and well-characterized S. aureus clinical strains belonging to ST239-SCCmecIII-t037 and ST228-SCCmecI-t041 clones at 3h and 24h post-infection (p.i). ATCC12598 was used as a control strain. Using Imaging Flow Cytometry analysis, we found that strains differently invaded osteoblasts after 3h and 24h: ATCC12598 internalized in 70% and 50% of cells, ST239-SCCmecIII in 50% and 45% and ST228-SCCmecI in 30% and 20%, respectively. ST239-III, during the infection period, exerted a significative cytotoxic activity due to the over-expression of hla and psmA and the increased expression of the genes involved in adhesion, probably due to the release and re-entry of bacteria inside MG-63 at 24h p.i. The lower invasiveness of ST228-I was also correlated with the non-cytotoxic activity inside osteoblasts. This clone was not able to activate a sufficient cellular reaction and succumbed in-side the MG-63 cells.