Significant number of MRSA had been isolated from patients at the ward of neonatal intensive care unit (NICU) /growing care unit (GCU) for two years. Since standard countermeasures by hospital manual were not effective to control the prevalence, additional strategy was conducted based on the analyses of risk factors for MRSA acquisition after admission. Independent risk factors for MRSA acquisition were admission to NICU [odds ratio (OR): 33.82, 95% confidence interval (CI): 2.43-470.39], use of open-bed (OR: 19.45, 95% CI: 3.94-96.49), and patients with cleft lip and palate (OR: 28.41, 95% CI: 1.75-460.74). Medical care by the staff other than NICU (P = 0.020) and conduction of rehabilitation (P = 0.002) were also selected by univariate analyses. Based on these results, several interventions were implemented. Compared with standard countermeasures period, MRSA acquisition rate was significantly decreased during additional strategy period [from 3.30 to 1.70/1000 patients day (P = 0.031) ]. In case of prolonged MRSA outbreaks in spite of vigorous standard management, additional new strategy should be introduced based on the assessment of the problems that caused outbreaks.