BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) has become a major pathogen of nosocomial infection. In Korea, incidence of MRSA is alarmingly high up to 70-80% of total S. aureus strains isolated from tertiary care hospitals. To investigate the mechanism of intra- and inter-hospital spread of MRSA, we evaluated the genetic relatedness of MRSA isolates recovered from 3 different hospitals in Korea. METHODS:30 MRSA isolates obtained from Samsung Medical Center(SMC), 37 MRSA isolates from Seoul National University Hospital (SNUH) and 40 MRSA isolates from Dankook University Hospital (DUH) were classified into clonal types on the basis of pulsed field gel electrophoresis(PFGE). RESULTS: Several PFGE patterns were predominant among the isolates from SMC(A-7/30[23.3%], B-6/30[20.0%], C-4/30[13.3%], G-3/30[10.0%]). The prevalent PFGE patterns were different between medical ICU(A-3/5[60.0%]) and newborn ICU(B-4/9[44.4%]). The major clone at SNUH was PFGE type A, which was identical with one of the dominant clones of SMC. The major clone at DUH was PFGE type B, which was identical with another dominant clone of SMC. Although MRSA strains from SMC, which caused clinical diseases belonged to major PFGE patterns more often than colonized strains, the association was not significant statistically. CONCLUSION: The presence of epidemic strains of MRSA suggests that epidemic MRSA clones may be originated from common sources and spread between different hospitals. Also, there may be virulence factors of stains or host factors, which could select specific strains.