Mastitis, infection and inflammation of the mammary gland, is a well-known problem in the dairy industry, affecting cows worldwide and causing considerable financial losses. Multiple bacterial species can cause mastitis and E. coli is often involved. Despite many years of mastitis research, no efficient measures exist to prevent or treat the disease, and only little is known about specific virulence factors of the bacteria. Our goal is to understand the molecular mechanisms of host-pathogen interactions in the mammary gland and relate them to disease processes, in hope that understanding these mechanisms will lead to development of novel tools to combat E. coli mastitis. Using genome sequencing and analysis of six clinical isolates, we found that type VI secretion system (T6SS) gene clusters are present in all. Furthermore, using unbiased screening of strains for reduced colonization, fitness and virulence in our murine mastitis model, we have identified in P4-NR strain a new pathogenicity island encoding the core components of T6SS and its hallmark effectors Hcp, VgrG and Rhs. Next, we have shown that specific deletions of T6SS genes reduced in vivo pathogenicity. Based on our results we hypothesize that T6SS is an important virulence mechanism of MPEC. To our knowledge, we are the first to describe relevance of T6SS in the pathogenesis of mastitis. We intend to validate our findings in dairy cows and field strains and to study the molecular mechanisms of T6SS associated with MPEC virulence. The identified mechanism may provide new targets for diagnostic, preventive and therapeutic intervention.