Decolonization of MRSA detected in the oral cavity and tracheal aspirates occurred in 85% and 58% of neonates, respectively, with nasal mupirocin treatment. Recurrent MRSA colonization occurred in 45% of neonates whose MRSA was detected in the oral cavity at a mean of 19 days. Recurrent MRSA colonization occurred in 58% of neonates whose MRSA was detected in tracheal aspirates at a mean of 23 days.