BACKGROUND: Staphylococcus aureus (S. aureus) possess a variety of virulence genes that are involved in the pathogenesis of infections caused by this agent. OBJECTIVES: The aim of this study was to evaluate the prevalence of the genes encoding collagen binding (cna) and fibronectin binding (fnb) adhesion factors in Staphylococcus aureus isolates from food and clinical specimens. METHODS: During the time period 2010-2013, a total of 38 isolates of Staphylococcus aureus from clinical specimens and 32 isolates from food samples were collected. All isolates were identified biochemically and subjected to DNA extraction. The accuracy of DNA extraction from each isolate was confirmed by PCR amplification of aroA gene and then the presence of cna and fnb genes in the extracted DNAs was assessed by PCR, using the specific primers. RESULTS: The results showed that among 38 isolates from clinical specimens, 15 (39.5%) & 32 (84.2%) and among 32 isolates of food origin 10 (31/2%) and 16 (50%) isolates had cna and fnb genes respectively. Thirteen clinical (34.21%) and 6 food isolates (18.7%) were positive for both fnb and cna genes and 4 clinical (10.5%) and 12 food isolates (37.5%) were lacking both genes. CONCLUSIONS: According to the results, it is concluded that, although these adhesion genes are not present in all Staphylococcus aureus clinical isolates, but their prevalence is high and using the products of these genes in vaccines may be effective in protecting against infections caused by this bacterium.