In Staphylococcus aureus aminoglycosides and methicillin resistances are closely associated. We aimed at detection of the prevalence of methicillin and aminoglycosides resistances in S. aureus isolated from surgical ICUs in Kasr Alainy hospitals, the association of mecA gene and aminoglycoside modifying enzymes (AMEs) genes among these isolates and the accuracy of cefoxitin disc diffusion method in relation to PCR. 150 clinical samples were collected. Cultivation and identification of isolates were done by the standard microbiological techniques. All S. aureus isolates were tested for methicillin and aminoglycosides resistance by disc diffusion method and for presence of mec A gene and AMEs genes by multiplex-PCR. 48 S. aureus were isolated (32%) with a high prevalence of mec A gene (89.58%) and AME genes (60.42%) and co-existance of mec A gene and one or more of AME genes in 60%. mec A gene was detected in 87% of cefoxitin resistant isolates and aac(6')-Ie+aph(2'') was the most predominant AME genes.