Introduction: MRSA: Major cause of health care associated infections (HA-MRSA). The alarming rise in the rates of HA-MRSA reported from this region necessitates the need for a DNA based assay. Real-time PCR: rapid platform or detection of MRSA. The study plans to compare culture to real-time PCR for the detection of MRSA directly in the clinical specimen Objectives: The present study aimed to isolate and identify MRSA from clinical specimen, to detect mec A gene in the clinical specimen and to compare direct detection of mec Agene with culture for Staphylococcus aureus Methods: Cross-sectional hospital based study was undertaken noninvasive samples (blood, deep tissue, aspirated pus, sterile body fluids) received for culture. The results of PCR and culture were compared in terms of sensitivity, specificity, PPV, NPV. Results: 110 non-duplicate clinical samples were included. MRSA rate: 29%. The rates of isolation were 74.6%: skin and soft tissue infections, 11% from blood stream infections, 10.4% from osteomyelitis cases, 4% respiratory secretions. Antibiotic resistance rates of MRSA ciprofloxacin(75%), clindamycin (51.1%), trimethoprim sulfamethoxazole (59.1%) and erythromycin (62.5%). 100% of the isolates were sensitive to Vancomycin. PCR for MRSA detection: Sensitivity: 97%, Specificity: 98% Discussion: This study demonstrates the utility of a rapid platform: real-time PCR for the detection of MRSA from clinical samples directly on the same day. The results of Gram stain were used as criteria for selection of samples.