Intramammary infection (IMI) is one of the most costly diseases to the dairy industry. It is primarily due to bacterial infection and the major intramammary pathogens include Escherichia coli, Streptococcus uberis, and Staphylococcus aureus. The severity and outcome of IMI is dependent on several host factors including innate host resistance, energy balance, immune status, parity, and stage of lactation. Additionally, the infecting organism can influence the host immune response and progression of disease. It is increasingly recognized that not only the infecting pathogen species, but also the strain, can affect the transmission, severity, and outcome of IMI. For each of 3 major IMI-associated pathogens, S. aureus, Strep. uberis, and E. coli, specific strains have been identified that are adapted to the intramammary environment. Strain-dependent variation in the host immune response to infection has also been reported. The diversity of strains associated with IMI must be considered if vaccines effective against the full repertoire of mammary pathogenic strains are to be developed. Although important advances have been made recently in understanding the molecular mechanism underpinning strain-specific virulence, further research is required to fully elucidate the cellular and molecular pathogenesis of mammary adapted strains and the role of the strain in influencing the pathophysiology of infection. Improved understanding of molecular pathogenesis of strains associated with bovine IMI will contribute to the development of new control strategies, therapies, and vaccines. The development of enabling technologies such as pathogenomics, transcriptomics, and proteomics can facilitate system-level studies of strain-specific molecular pathogenesis and the identification of key mediators of host-pathogen interactions.