Staphylococcus aureus represents a public health challenge all over the world. Therefore, this study aims to analyze the prevalence of five genes (sea, seb, sec, see and seg) encoding the staphylococcal enterotoxins in S. aureus isolated from different sources and to evaluate the association of these toxins in comparison to susceptibility towards 12 antimicrobials; antimicrobial susceptibility was conducted by disc diffusion method. Detection of staphylococcal enterotoxins was performed by PCR and the ability to express these genes was assessed among isolates by RT-PCR. The most common enterotoxin gene was sea gene (66%), followed by seb, sec, see and seg (38%, 23%, 19% and 5%) respectively. Expression of sea, seb and seg genes was variable. However, sec and see genes were not expressed by any of the tested isolates. No statistically significant association exists between (seb, sec and see) and isolation sources, while the sea was significantly associated with clinical isolates. High significant correlation was found between elevated sea expression and multidrug-resistance. Our findings indicate that the pathogenic potential of S. aureus may be greater than previously thought. This emphasizes the utmost need to implement proactive measures and more emphasis will be placed on the application of hygiene practices in hospitals to control S. aureus infection and enterotoxins production.