The increased mortality among patients with obstructive sleep apnea syndrome has been explained in part by the increased incidence of arterial and pulmonary hypertension. A decreased heart rate variability (HRV) has been shown to be associated with an increased mortality as well. We investigated 53 patients, admitted to the hospital for chest pain for sleep-related breathing disorders (SRBD) with an ambulatory screening device (MESAM-IV). HRV was recorded simultaneously. All patients received coronary artery catheterization and 36 had significant coronary artery disease (CAD; 67.9%). Standard time domain parameters were compared by a 4-way Anova for patients with an oxygen desaturation index of more and less than 5/hour and 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 (38.0 ± 29.0 vs. 59.2 ± 51.5 ms; p < 0.05) were significantly decreased in patients with SRBD. In an hourly breakdown the number of desaturations was not correlated with a change in HRV. Mean oxygen saturation was significantly decreased in patients with SRBD (95.2 ± 1.8 vs. 96.2 ± 1.42%, p < 0.05), and positively correlated with the pNN > 50 (r = 0.34, p < 0.01). This correlation might suggest a more profound pathophysiological interaction between HRV and SRBD than short-term vagal activation alone. The results favor HRV for inclusion in future risk stratification models in patients with sleep apnea syndrome.