Background: Staphylococcal enterotoxins (SEs) are family members of more than 20 different staphylococcal and streptococcal exotoxins. SEA and SEB are the most common toxins in staphylococcus-related food poisoning. Objectives The present study aimed to estimate the prevalence of SEs Methicillin-Resistant Staphylococcus aureus (MRSA) isolated from different clinical samples. Methods:  A cross-sectional laboratory-based study was conducted from November 2020 to January 2021. To isolate and identify S. aureus, the conventional method and protein A latex test were used. MRSA was detected using methicillin (MET 5μg) by using the Kirby-Baur disk diffusion method. Extracted DNA was amplified for the specific Staphylococcal enterotoxins (SE) gene to confirm the SEA, SEB and SEC. Result: The SEA gene was observed among 120 (100%) clinical isolates. The combined staphylococcal enterotoxin genes A, B and C were found in 33.3% of the isolates. Respiratory tract infection (RTI) shows the highest percentage of SEA 28.3%. Conclusion: The present study showed a high prevalence of SEA in clinical settings at Khartoum State. A high prevalence of the combination of more than one gene occur in SEA with SEC, which was represented 82.5%. The present study showed a strong relationship between MRSA and SEA that could be due to a specific strain of MRSA carrying the SEA gene. Further studies should be done about Staphylococcal enterotoxins.