Abstract: The aims of present investigation were to study the nasal carriage rate of MRSA in hospital staff and in-patients, determination of antibiotic resistant patterns of nasal and clinical MRSA isolates and typing of MRSA isolates by RAPD- PCR. Two hundred and six S. aureus isolates were recovered from clinical specimens and noses of 460 staff and in-patients admitted in Imam Khomeini and Pediatrics hospitals by standard methods during 6 months (2004-2005). Disk agar diffusion (using 13 antibiotics disks) and oxacillin agar screening methods for detection of MRSA isolates were performed according to CLSI. PCR was also used to amplify a 310 bp sequence from S. aureus genome (mecA gene) for detection of MRSA isolates. RAPD-PCR was carried out for fingerprinting of MRSA isolates genome. MRSA isolates were resistant up to 11 antibiotics. All of the MRSA isolates were resistant to penicillin, but sensitive to vancomycin. Of 206 S. aureus isolates, 77 MRSA isolates were detected using disk agar diffusion and oxacillin agar screening methods. In contrast, 80 isolates were detected as MRSA by amplification of mecA sequence. In RAPD-PCR experiments, 43 different RAPD patterns were obtained from our MRSA isolates. Nasal carrier rate of S. aureus was 34.7% and MRSA isolates were high (38.8%) in our hospitals. This study revealed high rate of MRSA, that infected patients and MRSA nasal carriers (staff and in-patients) were the main source of transmission and infection, therefore effective control measures are necessary to avoid nosocomial infection outbreaks.