Abstract Forty-five neonates who carried methicillin-resistant Staphylococcus aureus (MRSA) were studied. Retrospective molecular analysis using pulsed-field gel electrophoresis showed three separate MRSA epidemics in the nursery. Strains of MRSA isolated from the neonates were also isolated from the hospital environment and health care providers. Clinical manifestations included skin pustules (eight patients), conjunctivitis (four patients), or other minor infections (two patients). No neonate developed systemic infection. The prevalence of MRSA decreased with age. At one year, three (14·3%) of 21 infants that had carried MRSA at six days remained carriers and only two (1·1%) of 180 infants in a control ‘ S. aurems-negative at six days’ group carried MRSA.