Obstructive sleep apnoea syndrome (OSAS) is associated with inflammatory processes and elevated plasma cytokines. This study assesses the effect of surgery in cytokine levels of OSAS patients. A total of 24 male patients with mild to moderate OSAS, confirmed with polysomnography underwent septoplasty and uvulo-palato-pharyngoplasty in a period of a year. Control group consisted of 12 overweighted subjects and 15 obese subjects. Peripheral venous blood was collected from each patient 1 week before surgical treatment and 6 months postoperatively. Spontaneous production of tumour necrosis factor (TNF-a) by monocytes and serum levels of IL-1beta and IL-6 were investigated. Control subjects were also examined for the same pro-inflammatory cytokines. Production of TNF-a and IL-6 were significantly elevated in OSAS patients and obese controls compared with overweighted control subjects (p < 0.05). Serum levels of IL-1beta did not differ among the study groups. Preoperative cytokine values were significantly correlated with the preoperative body mass index (BMI) and the apnoea/hypopnoea index (AHI) in OSAS patients. Surgery resulted a significant reduction in the TNF-a and IL-6 values of the study group. Decrease in cytokine level was strongly correlated with the AHI decrease. The postoperative relative percentage change of IL-6 values was significantly higher than this of TNF-a (p < 0.001). Surgical management of mild to moderate OSAS leads to a significant reduction in TNF-a and IL-6 values. Our data indicate that AHI is an independent risk factor of systemic inflammation; however it affects cytokines to a lesser degree compared with the BMI.