Background: Whether mice are an appropriate model for S. aureus infection and vaccination studies is a matter of debate, because they are not considered as natural hosts of S. aureus. Sparked by an outbreak of S. aureus infections in laboratory mice, we investigated whether laboratory mice are commonly colonized with S. aureus and whether this might impact on infection experiments. Methods: We characterized 99 S. aureus isolates from laboratory mice (spa typing, virulence gene PCR), and quantified murine antibodies using FlexMap technology. Results: Specific-pathogen-free mice from various vendors were frequently colonized with S. aureus (0-21%). S. aureus was readily transmitted from murine parents to offspring, which became persistently colonized. Most murine isolates belonged to the lineage CC88 (54%). Murine strains showed features of host adaptation, such as absence of hlb-converting phages and superantigen genes, as well as enhanced coagulation of murine plasma. Importantly, S. aureus colonization induced a systemic IgG response specific for numerous S. aureus proteins, including several vaccine candidates. Conclusion: Laboratory mice are natural hosts of S. aureus and, therefore, provide better infection models than previously assumed. Pre-exposure to S. aureus is a possible confounder in S. aureus infection and vaccination studies.