Carriage of S. aureus in the anterior nares seems to play a significant role in the pathogenesis of infection. This study aimed to determine the molecular characteristics and antibiotic susceptibility pattern of S. aureus isolates obtained from the nasal carriage of health care workers (HCWs). This study was performed during July 2014 to July 2015 at three tertiary care hospitals. Nasal samples were collected from the nasal cavity of HCWs. Standard microbiological methods were used for identification of S. aureus isolates. Antibiotic susceptibility pattern was determined by the disc diffusion method. Determination of SCCmec typing and virulence genes was performed by the PCR method. From the isolates of 340 nasal swab samples of HCWs, 65 S. aureus strains (19%) including 22 (33.8%) MRSA were isolated. The highest sensitivity for MRSA isolates was towards vancomycin and rifampicin, each with 90.9%. Overall, 17% (11/65) and 92.3% (60/65) of S. aureus isolates were positive for pvl and hla genes, respectively. The rates of SCCmec types II, III, IV, V and I among MRSA isolates were 36.4 %, 22.7 %, 22.7 %, 9.1% and 4.5% respectively. The results of the present study indicate that S. aureus nasal carriage with potential virulence ability still remains a significant healthcare problem, especially in hospital environments.