Background: Determining the etiologic causes of septic arthritis is of the most importance. Goal of this study was to investigate presence of staphylococcal enterotoxins A, B, C and Toxic Shock Staphylococcal toxin-1 in the synovial fluid of patients with arthritis. Methods: This cross-sectional study was performed in the Pediatric and Orthopedic Wards of Hazrat Rasoul Hospital in Tehran, Iran during 2008- 2010. Gram stains, conventional cultures, direct detection of soluble bacterial antigens were used to detect H. influenza, S. pneumonia, group B streptococci, and N. meningitidis while Latex particle agglutination test was used for staphylococcal supper antigens (by enzyme immunoassays) upon synovial fluid tapping of 62 individuals (5 mo to 16 yrs, mean=11 3.8 yrs). P<0.05 was considered statistically significant. Results: Positive SF cultures (n=11): 5 positive cases of S. aureus; 5 S. pneumonia; 1 H. influenza, and 1 Klebsiella. Positive gram stains: 10%; and positive LPA: 4%. Staphylococcal arthritis was diagnosed in 7 (39%) cases upon positive culture or positive gram stain. The most common type was TSST-1 (47%) and the least common was enterotoxin B (18%). Isolation of S. aureus (positive culture) was correlated to presence of enterotoxin A in synovial fluid but not to enterotoxins B, C or TSST-1. Conclusion: Staph. aureus had a prominent role in arthritis. 47% of cases with negative culture for S. aureus had at least one type of staphylococcal super antigens in the synovial fluid. Searching for antigens of usual organisms or staphylococcal supper antigens could be helpful for diagnosis and subsequent treatment.