Background: The emergence of resistance to methicillin resistant Staphylococcus aureus (S.aurus) (MRSA), followed by Vancomycin resistant S.aurus has turned the therapy of staphylococcal infections into a worldwide challenge. Three classes of vancomycin-resistance have emerged that differ in vancomycin susceptibility; vancomycin resistant S.aureus (VRSA), Vancomycin intermediate S.aureus (VISA) and heterogenous vancomycin-Intermediate S.aureus (hVISA). Objectives: The present study aimed to detect S.aureus with reduced susceptibility to vancomycin in different types of clinical samples and their genomic characterizations. Methodology: The study was carried out on 250 S.aureus isolates from different types of clinical samples collected from patients admitted to various departments in the Alexandria University Hospitals, Egypt from May 2014 to April 2015. Results: We detected 22 S.aureus isolates with reduced sensitivity to vancomycin out of the 250 S.aureus test isolates by PAP-AUC and agar dilution methods. Three of them were VISA and 19 were hVISA; mainly isolated from pyogenic infections. Molecular typing of VISA and hVISA exhibited dominance of agr group Type I. Conclusion: Strict infection control measures and antibiotic policy should be adopted to control the problem of VISA and hVISA.