Inflammatory cytokines such as interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha) may have a direct effect on glucose and lipid metabolism. On the other hand, it is known that IL-6 and TNF-alpha are important pro-inflammatory cytokines in the pathogenesis of atherosclerosis. The goal of present study was to test whether sleep apnea contributes to the previously reported increases of IL-6 and TNF-alpha independent of obesity. Forty-three obese (body mass index, BMI>27 kg/m2) men with newly diagnosed obstructive sleep apnea syndrome (OSAS) (apnea-hypopnea index, AHI> or =5) and age- and BMI-matched 22 obese nonapneic male controls (AHI<5) were enrolled in this study. To confirm the diagnosis, all patients underwent standard polysomnography in the sleep disorders center. Serum samples were taken at 08:00 h in the morning after overnight fasting. Serum IL-6 and TNF-alpha levels were found significantly higher in OSAS patients than in controls (p=0.002, p=0.03). Serum IL-6 and TNF-alpha levels were significantly correlated with AHI in OSAS patients (r=0.03, p=0.046 and r=0.36, p=0.016). There was no significant correlation between serum IL-6, TNF-alpha levels and AHI in controls. Serum IL-6 and TNF-alpha levels were not correlated with BMI both in OSAS patients and controls. In conclusion, circulating IL-6 and TNF-alpha levels in patients with OSAS, as independent of BMI are significantly higher than levels in controls and there is a positive relationship between previously mentioned cytokines' levels and the severity of OSAS. According to these results, the link between cardiovascular morbidity and OSAS may be explained by the coexistence of other cardiovascular risk factors such as circulating IL-6 and TNF-alpha levels.