Background Staphylococcus aureus is recognized as an important cause of food poisoning related to the consumption of raw, undercooked, or mishandled foods worldwide. Methods A total of 90 individual meat samples and 200 clinical specimens were collected and investigated the frequency of S. aureus and classical enterotoxin genes. The samples were cultured on Baird-Parker and Mannitol salt agar and subjected for confirmatory biochemical tests and molecular detection of femA, sea, seb, sec, sed, and see genes. Results A total of 31 (34.5%) meat samples and 81 (40.5%) clinical specimens were positive for the presence of S. aureus. These isolates were detected with slightly higher frequency in clinical specimens than food samples (P> 0.05). Furthermore, the frequency of S. aureus in raw meat (23.4%) was higher than that in cooked meat samples (11.1%) (P< 0.05). Staphylococcal enterotoxin (SE) genes were identified in 18 (58.1%) of 31 meat isolates and 42 (51.8%) of 81 clinical isolates. The frequency of SE genes (except see) in meat isolates was slightly higher than that in clinical isolates (P> 0.05). We found sea and see genes with higher frequency than others in both meat and clinical samples. Furthermore, 55.5% of meat isolates and 38.1% of clinical isolates possessed more than one se gene. Conclusion Detection of enterotoxigenic S. aureus in clinical and raw meat samples shows a probable risk for public health. Therefore, intensive and continuous monitoring of potentially pathogenic S. aureus is strongly recommended in order to evaluate the human health risk arising from food consumption.