Staphylococcus aureus isolates were isolated from fifty clinical samples collected from Ain Shams University Hospitals (March - July 2016) and identified using biochemical and microbiological tests. PCR was performed using specific primers to determine the isolates of Methicillin - Resistant Staphylococcus aureus (MRSA) based on the presence of mecA gene. Thirty-four isolates from total fifty isolates (68%) were identified as MRSA isolates. To study the genotoxicity for this isolates, forty-five mice were injected with these MRSA isolates and comet and micronuclei assays were performed on mice liver tissues and bone marrow respectively. These assays revealed 24% - 22% DNA damage as an indicator for chromosomal breakage by comet and micronucleus assays respectively which indicate that infection with these isolates leads to mutations. Studying these isolate furthermore will give an insight on how critical maintaining high standard hygiene in Egyptian hospitals and attention to infection control system can prevent occur of outbreaks