Methicillin-resistant Staphylococcus aureus (MRSA) is well known as one of the most frequent etiological agents of healthcare-associated infections. The epidemiology of MRSA is evolving with emergence of community-associated MRSA, the clonal spread of some successful clones, their spillover into healthcare settings and acquisition of antibacterial drug resistances. Neonatal intensive care unit (NICU) patients are at an especially high risk of acquiring colonization and infection by MRSA. Epidemiology of MRSA in NICU can be very complex because outbreaks can overlap endemic circulation and make it difficult to trace transmission routes. Moreover, increasing prevalence of community-associated MRSA can jeopardize epidemiological investigation, screening and effectiveness of control policies. Surveillance, prevention and control strategies and clinical management have been widely studied and are still the subject of scientific debate. More data are needed to determine the most cost-effective approach to MRSA control in NICU in light of the local epidemiology.