Background: Methicillin Resistant Staphylococcus aureus (MRSA) is a common major human pathogen that causes hospital-acquired infections. Characterization and typing of the staphylococcal cassette chromosome has led to a better understanding of MRSA infection cycle in hospital. The mecA-associated hypervariable region size classifies MRSA isolates that colonized in nasal carriers. Objectives: The aim of this study was to compare the genetic background of hypervariable region (HVR) of mecA gene in S. aureus isolated from nasal carriers and clinical samples. Materials and Methods: A cross sectional study was performed on 261 nasal swabs collected from healthy health care workers (HCW) and 109 clinical samples from Tehran university hospitals. All the S. aureus isolates were identified by biochemical tests (Coagulase, Catalase, Manitol fermentation, and DNase tests). S. aureus isolates were investigated for the variability of HVR of mecA gene by PCR method. Results: Among 261 collected nasal swabs, 70 (27%) were S. aureus. Of these, 29(41%) isolates were resistant to Oxacillin and 32 (46%) of those had mec-HVR gene. The polymerase chain reaction (PCR) products showed five different patterns of HVR. Also among 109 clinical samples, 52 (48%) of them were S. aureus. Of these, 40 (77%) were resistant to Oxacillin and 45 (87%) of them carried the mec-HVR gene. The PCR products showed 11 different patterns of HVR. Conclusions: Molecular typing of MRSA isolates by HVR amplification has shown a high diversity among the strains and can be used as a basis for tracking the contaminations and the source of hospital infections from staff to patients and vice versa.