Background: Staphylococcus aureus, particularly methicillin-resistant (MRSA), is an important pathogen in neonatal intensive care units (NICUs). Carriage of S. aureus is a significant risk factor for subsequent infection. Objectives: To determine the current status of MRSA prevalence among NICU-hospitalized infants in Taiwan, we conducted this pilot island-wide survey. Methods: On two designated dates in 2011, each patient who stayed in the NICUs of 7 participating hospitals was included. Nasal and umbilical swabs were obtained and sent for detection of S. aureus. The prevalence and risk factors for MRSA carriage were analyzed. MRSA strains were tested for antimicrobial susceptibility and underwent molecular characterization. Results: A total of 251 subjects were included. The overall prevalence of S. aureus and MRSA carriage was 13 and 4.4%, respectively. Previous skin and soft tissue infection was the only predictor in multivariate analysis (OR 40.36; 95% CI 2.32-702.64; p = 0.011). Among 11 MRSA isolates, 3 pulsotypes were identified, with one major type (73%). Nine isolates carried a type IV staphylococcal chromosomal cassette, and 2 carried the type VT. All but one MRSA isolate belonged to linage sequence type 59, the community clone in Taiwan. Conclusions: On a designated date, 4.4% of the infants staying in NICUs in Taiwan carried almost genetically identical community strains of MRSA. MRSA colonization in these infants was significantly associated with previous skin and soft tissue infection.