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Background: Bacteria induced sepsis is common in infants and children. Staphylococcus aureus produces numerous exotoxins, like staphylococcal Toxic shock syndrome toxin (TSST- 1), which stimulate the immune system by T cell activation and inflammation in various organs. Recent studies suggest that staphylococcal toxins, generally named super antigens (SAgs), may also have a significant role in the pathogenesis of some pediatric disorders especially in the clinical presentation of sepsis and septic shock. This study was carried out in order to compare staphylococcal TSST- 1 (SAgs) in children with sepsis symptoms (and septic shock) with negative blood culture versus a control group. Materials & Methods: This cross-sectional study was conducted during 2 years (2014 -2016) in two referral hospitals (Rasoul Akram and Bahrami hospitals) in Tehran, Iran. We selected 44 children) mean age of 4 years) who were admitted in pediatrics and PICUs wards with sepsis symptoms- /+septic shock. Forty-five children (mean age of 3.9 years) were selected as a control group. All cases with blood samples were examined for TSST-1 (SAgs) by polymerase chain reaction (PCR) method in both case and control groups and results were compared. Data were analyzed by SPSS-16software. Chi-square or Fisher test was used to compare the variables. P-value < 0.05 was considered as a valuable tool. Results: Positive blood cultures with other bacteria, Streptococcus pneumonia, Haemophilus influenzae, Pseudomonas aeruginosa, Escherichia coli, were detected in 5 cases with negative TSST-1 in blood samples. S.aureus isolated from blood culture was detected in 2 cases with positive TSST- 1.Positive TSST-1 (SAgs) was detected in 6 cases (14%) with negative blood culture for S.aureus; it was significantly higher in cases (14% vs. 2%; P value = 0.05). Conclusion: This study indicates the probable role of TSST-1(SAgs) in the progression of sepsis (and septic shock) in toxic children with negative blood culture for S.aureus. Anti-staphylococcal treatment is immediately required, especially in toxic children with related clinical presentations, even in cases with negative blood cultures. Indeed, the clinical use against SAgs suppressants of downstream cell-destructive events might be helpful.