The increased mortality among patients with obstructive sleep apnoea syndrome has been explained in part by the increased incidence of pulmonary hypertension and coronary artery disease (CAD). A decreased heart rate variability has been shown to be associated with an increased mortality as well. We therefore screened 53 patients for sleep-related breathing disorders (SRBD) and heart rate variability (HRV) during the sleeping period. Standard time domain parameters were compared in a univariate multifactorial model for patients with an oxygen desaturation index (ODI) of more or less than 5 including the factors CAD, diabetes and beta-blocker use. The percentage of differences between RR-intervals that differ more than 50 ms (pNN > 50: 9.0 +/- 11.1% vs 19.2 +/- 22.2%; p < 0.05) as well as the root mean square of these differences (rMSSD: 38.0 +/- 29.0 msec vs 59.2 +/- 51.5 msec; p < 0.05) were significantly decreased in patients with SRBD. These results favour HRV for inclusion in future risk stratification models in patients with sleep-related breathing disorders.