Staphylococcus aureus have been associated with a wide range of serious community-and hospital-related infections worldwide. The molecular characterization of these isolates is of both clinical and infection control importance. In this context we studied the virulence determinants among ninety three methicillin resistant S. aureus (MRSA) and 37 sensitive (MSSA) isolates recovered at a major tertiary care medical center in Lebanon in relation to their enterotoxin genes (sea, seb, sec, sed, see, seg, she, sei, sej), and toxic shock syndrome toxin-1 gene (TSST-1) using multiplex PCR. The prevalence among MRSA vs MSSA for these genes were: sea (22% vs 35%), seb (65% vs 14%), sec (3% vs 8%), sed (14% vs 3%), see (0% vs 0%), seg (11% vs 60%), seh (5% vs 11%), sei (52% vs 78%), sej (1% vs 3%), and TSST (0% vs 19%). All TSST-1 positive isolates (n=7) were MSSA with one isolate being additionally positive for Panton-Valentine Leukocidin (PVL) gene. The sequencing of the polymorphic X region of the protein A (spa typing) in 33 of the isolates (28 MRSA vs 5 MSSA) revealed that the most common spa types among the MRSA isolates were t044 (64%), t037 and t537 (7% each), while 5 different spa types were detected among these MSSA isolates. This study is considered the first to demonstrate the virulent genes and genetic diversity of S. aureus isolates in this country. It addition, it revealed the high incidence of some of the tested virulent determinants such as seb and sei genes among MRSA and seg and sei genes among MSSA isolates, which are important findings for epidemiologic and infection control aspects.