Aim: This study aimed to investigate the superantigenic (SAg) toxin, exfoliative toxin (ET), hemolysin (HLY), leukotoxin (LUK) genes and accessory gene regulator (agr) types in Staphylococcus aureus isolates from various clinical materials. Material and Methods: A total of 190 S. aureus isolates were investigated for the presence of toxin genes, mecA gene and agr types using by polymerase chain reaction (PCR). Results: mecA gene was detected in 87 (45.8%) isolates. Of the 190 S. aureus isolates examined, 83.7% (n=159) were found to be positive for SAg genes. The seg (41.1%) was determined to be the most common toxin gene, followed by sei (38.9%), selo (38.9%), selm (28.4%), sea (%25.8), and tst (18.4%) genes, respectively. Seventy one different SAg toxin profiles were identified. Type I νSaβ encoding seg, sei, selm, seln and selo was the most common mobile genetic element (MGE), which was detected in 37 isolates (19.5%). The hla, hlb, hld, hlg and hlg2 genes were detected in 92.6% (n=176), 1.6% (n=3), 98.9% (n=188), 1.1% (n=2) and 31.6% (n=60) of the isolates, respectively. The pvl gene was detected in 12.6% (n=11) of methicillin resistant S. aureus (MRSA) and 14.6% (n=15) of methicillin sensitive S. aureus (MSSA), respectively (p=0.701). While none of the isolates carried lukM gene, 67% (n=69) of MSSA and 69% (n=60) of MRSA isolates were found to be positive for lukED gene (p=0.519). Conclusion: High occurrence and diversity of toxin genes among S. aureus isolates could be explained by horizontal transmission of toxin genes through MGEs.