Staphylococcus aureus is one of the most common pathogens isolated from clinical specimens in many hospitals worldwide. The objectives of the present study was to determine the trends of the S. aureus isolated from clinical specimens and to detect the virulence genes of S. aureus namely mecA, LukS, can, icaA, SdrE and hlg. Data of S. aureus isolation in Hospital Universiti Sains Malaysia (HUSM) from 2002-2014 which is available in our WHONET system was analyzed. Staphylococcus aureus isolates were randomly collected from the archived culture and the virulence genes were detected by PCR. A total of 15176 S. aureus were isolated and reduction in the MRSA was observed during the study. This study showed that S. aureus infection is still an unresolved issue, where clinical specimen from swab contributes the highest number. The percentage of MRSA also is fluctuating and serves as a good indicator for a more vigilant infection control activity in the hospital setting.