Methicillin-resistant Staphylococcus aureus (MRSA) is an evolving cause of illness and death worldwide. MRSA strains can express a wide range of virulence factors that are implicated in their pathogenicity. The present study aimed to investigate the prevalence of crucial virulence traits encoding genes among MRSA isolates from Egyptian hospitals. A total of 170 S. aureus isolates were identified in this study from two Egyptian hospitals. These isolates were recovered from different clinical samples, during the period from September 2017 to December 2018. Of the 170 isolates, 138 (81.2%) were identified as MRSA by conventional microbiological methods and the identification was confirmed by the detection of methicillin resistance encoding gene mecA. Antimicrobial susceptibility was determined for MRSA isolates using the Kirby-Bauer disk diffusion method against 16 different antimicrobial agents representing diverse antimicrobial classes. Out of 109/138 (79%) Multidrug-resistant (MDR)-MRSA, fifty MDR-MRSA isolates were selected for further analysis of virulence encoding genes. MRSA isolates were resistant to different classes of antimicrobial agents including ꞵ-lactams, aminoglycosides, tetracyclines, macrolides and lincosamides. The antimicrobial resistance patterns among the selected 50 MDR-MRSA isolates revealed that the highest resistance rate was 100% to each of cefoxitin and penicillin, followed by doxycycline (80%), tetracycline (76%), gentamicin (74%), erythromycin (68%), clindamycin (60%) and azithromycin (50%). While the highest susceptibility rate was 88% to linezolid, followed by teicoplanin (66%), and amikacin (60%). Among the selected MDR-MRSA isolates, 52% were strong biofilm producers and 48% were moderate biofilm producers. The 50 MDR-MRSA isolates were screened for the presence of the virulence genes (icaA, icaD, cna, hla, geh, tsst-1 and LukE/D)that areimplicated in their pathogenicity. The highest frequency of virulence genes in the selected MDR-MRSA isolates was 100% to each of icaD and geh, followed by hla (98%), icaA (96%), cna (92%), LukE/D (68%), and tsst-1 (56%). This study indicates that MRSA infection remains a significant problem in hospitals in Egypt. In addition,  this study has verified a high prevalence of virulence factors among MRSA isolates from diverse clinical sources. Therefore, future studies on MRSA should aim to elucidate MRSA epidemiology, study antimicrobial susceptibility profiles, and investigate their virulence factors for effective control measures and better health management.