Background: In this study we aimed at detecting the enterotoxin A and B gene of S. aureus in clinical samples of patients attending health centers in Zahedan using molecular methods.

Materials and Methods: A cross-sectional study was carried out in which 40 samples of S. aureus were obtained from patients in a hospital in Zahedan, Iran. Following the biochemical tests, Identifications were confirmed by PCR with specific primers.

Results: Among 40 clinical isolates of S. aureus the frequency of sea gene was 2% and the frequency of seb gene was 8% while the frequency of both sea+seb genes was 3%.

Conclusion: Enterotoxin of S. aureus is one of the main factors in the pathogenesis of various diseases and production of these toxins increase the incidence of diseases, so rapid treatment is needed for enterotoxin gene expression.