Heart rate variation (HRV) reflects the activity of the autonomic nervous system. The aim of the study was to analyze HRV in obstructive sleep apnea (OSA) and obesity hypoventilation (OH) patients to answer the question of whether chronic alveolar hypoventilation influences autonomic heart rate regulation. In 41 patients, diagnosed with either \'pure\' OSA (n=23, apnea/hypopnea index--AHI: 43.8+/-18.0 PaCO2</=45 mmHg) or OH syndrome (n=18, AHI 58.7+/-38.0 PaCO2>46 mmHg), the HRV was analyzed, based on an 8 h ECG recording during sleep. In the OH patients, compared with the OSA patients, there was a globally decreased HRV, with a corresponding decrease in high frequency power in the spectral analysis of HRV and increased low frequency/high frequency ratio (p<0.05), indicating a reduced parasympathetic and increased sympathetic heart rate modulation. We conclude that hypoxemia and hypercapnia of the sleep disordered breathing have an impact on the autonomic heart rate regulation. HRV indices have a potential to become prognostic factors for the development of cardiovascular complications in patients with sleep disordered breathing.