To determine the prevalence of aminoglycoside-modifying enzymes (AMEs) genes and the rate of resistance to amikacin, gentamicin, kanamycin and tobramycin a total of 1228 gene. The rate of resistance as determined by disk diffusion method and Etest was 48.2% for kanamycin, 48.2% for amikacin, 12.9% for tobramycin and 6.3% for gentamicin. MRSA were more resistant than MSSA (92.7% resistant to amikacin and kanamycin, 25% to tobramycin and 12.3% to gentamicin versus 2.6% to amikacin and kanamycin and 0.3% to tobramycin respectively). Vitek 2 P549 card failed to characterize all S. aureus that carried the aph(3')-IIIa gene. Significant differences on the rate of resistance and distribution of AME genes were observed among S. aureus strains originating in different hospitals. On the other hand, 42.8% of S. epidermidis, all methicillin-resistant, carried any AMEs genes; 70% of the positive strains carried the aac(6')-Ie-aph(2") gene in combination with both ant(4')-Ia and aph(3')-IIIa genes, 18% carried the aac(6')-Ie-aph(2") gene with ant(4')-Ia, while, 12% carried the aac(6')-Ie-aph(2") gene with aph(3')-IIIa. The rate of resistance to all aminoglycosides tested was 42.8%; 100% concordance of susceptibility results was observed between those of disk diffusion method, Etest and Vitek 2 P549 card. No significant differences on the rate of resistance or the AME gene distribution among different geographic regions were observed among S. epidermidis strains. These results suggest an alarming rate of aminoglycoside-resistant staphylococciin Greece and the necessity for a continuous surveillance.