The aim of this study was to assess the function of the autonomic nervous system in patients with obstructive sleep apnoea syndrome (OSAS). The study was designed as a cross-sectional case-control study. Fifty-one patients were included, and the findings were compared with those in 66 controls. Spectral analysis of heart rate variability (HRV) during supine rest, during controlled breathing and after tilting was performed in each patient and control case. The patients performed overnight sleep recordings the night before the HRV recordings. Individuals with an apnoea-hypopnoea index (AHI) above 20 were regarded as OSAS patients and those with AHI lower than 20 as snorers. Differences in HRV and blood pressure between patients and controls were analysed by multiple linear regression with age, body mass index and sex as independent variables. During free and controlled breathing there was a significant decrease in indices reflecting vagal modulation, indicating parasympathetic dysfunction in OSAS patients compared with controls. The mid-frequency component was also significantly reduced in OSAS patients after tilting but not in the lying position. This may be related to the parasympathetic dysfunction, but could also indicate a decreased sympathetic reserve capacity. We found no significant relation between AHI and indices of vagal modulation in the patient group. Our findings show an autonomic dysfunction in patients with OSAS. The dysfunction involves the parasympathetic system, and may be related to the increased cardiovascular mortality and malignant arrhythmia described in OSAS.