Obstructive sleep apnea (OSA) is a common disorder that has been associated with hypertension and ventricular arrhythmias. The aim of this study was to investigate changes in RR and QT intervals after respiratory and spontaneous arousals in patients with OSA. We conducted overnight sleep studies in 20 patients. The mean and range of respiratory disturbance index were 49 ± 28 and [17-107], respectively. During stage 2 sleep, ECGs were analyzed over a period of 30 seconds. From the 187 arousals investigated (120 respiratory vs. 67 spontaneous) a significant number were associated with a RR interval shortening (64%). Eighteen percent of the RR intervals were prolonged, with a significantly higher number during spontaneous arousals (13% vs. 27%). Similarly, QT intervals shortened after arousal (65%). But there were no significant differences between spontaneous and respiratory arousals. In conclusion, spontaneous and respiratory arousals lead to changes in heart rate and ventricular re-polarization.