Staphylococcus aureus is one of the main causes of foodborne diseases and a leading cause of nosocomial infections worldwide. Eleven (11) isolates from milk; 34 from meat and 23 of clinical source were subjected to phenotypic and biochemical characterizations for confirmation and further analysis for the presence of virulent genes, clonal relatedness and cytotoxicity profile. All isolates were positive for catalase production; 3, 11, and 7 isolates from milk, meat and clinical sources were coagulase positive. Polymerase chain reaction technique was used for the detection of 16S rRNA, clumping factor (cflA) and methicillin resistance (mecA) virulent genes. All isolates were positive for 16S rRNA; 100 and 45% of clinical; 73 and 64% of milk and none of the meat isolates were positive for cflA and mecA genes, respectively. Eight SmaI-based pulse-field gel electrophoresis (PFGE) clusters were identified at 80% similarity. Cytotoxic potential of the strains showed that 27.8, 24.1 and 22.2% of the strains tested had high, medium and low lactate dehydrogenase (LDH) release, respectively. These findings clearly demonstrate the presence of S. aureus in food and also in clinical infections, thus it should be a public health concern because even when virulent genes were not amplified in some strains, there may still be cytotoxicity effects.