This study highlights the prevalence of mecA and class1 integronin multidrug resistant Staphylococcus aureus. A hundred clinical Staphylococcus aureus (SA) isolates were collected from two Egyptian hospitals (Ain-shams hospital and Abbassia fever hospital).  All isolates were multidrug resistant (showing resistance to two or more antibiotic groups), antimicrobial susceptibility test showed that all isolates were resistant to methicillin, 46% were resistant to ciprofloxacin, 45% were resistant to erythromycin, 37% were resistant to vancomycin and 36% were resistant for imipenem and 11% were resistant to the seven tested antibiotic groups. Minimal inhibitory concentration showed that 58% of the isolates were resistant to imipenem. The isolates were examined for the presence of mecA, integrase gene (intl1) and class1 integron by PCR amplification. Forty two percent of the isolates were found to carry class1 integron gene cassette with variable amplicon, 36% of the isolates carried (intl1) integrase gene. Only 80% of methicillin-resistant S. aureus (MRSA) isolates were shown to have mecA gene.