To determine whether surgery influences cardiovascular autonomic modulation in obstructive sleep apnoea syndrome (OSAS), the present study was performed to evaluate the effect of upper airway (UA) surgery on heart rate variability (HRV) using frequency domain analysis for patient groups who have had either successful or unsuccessful surgery. We compared body mass index (BMI), polysomnographic [apnoea index (AI), apnoea-hypopnoea index (AHI), minimum SaO(2)] and HRV [very low frequency (VLF) power, low frequency (LF) power, high frequency (HF) power, HF/LF ratio, LFnu = LF/(LF + HF), HFnu = HF/(LF + HF)] parameters between the unsuccessful (n = 14) and successful (n = 22) surgical groups before and after UA surgery. Significant changes were observed for the successful patient group with respect to mean AI (from 29.1 +/- 21.3 to 2.0 +/- 3.2 events h(-1), P < 0.001), AHI (from 38.6 +/- 20.0 to 5.6 +/- 5.1 events h(-1), P < 0.001), minimum SaO(2) (from 73.3 +/- 12.7 to 86.3 +/- 6.5%, P < 0.001), VLF power (from 25599 +/- 12906 to 20014 +/- 9839 ms(2), P = 0.013), LF power (from 17293 +/- 7278 to 14155 +/- 4980 ms(2), P = 0.016), LFnu (from 0.700 +/- 0.104 to 0.646 +/- 0.128, P = 0.031) and HFnu (from 0.300 +/- 0.104 to 0.354 +/- 0.128, P = 0.031); however, mean BMI, HF power and LF/HF ratio did not change significantly after UA surgery. No significant changes were observed in the unsuccessful surgical group. Successful UA surgery may improve cardiac sympathetic and parasympathetic modulation in patients with OSAS.