The objective of this study was to examine heart rate variability (HRV) among sleep stages in obstructive sleep apnea (OSA) patients. The study was retrospective within subjects and examined the sleep stages and HRV in relation to OSA, age, body mass index (BMI), and sex. Data collected during diagnostic polysomnograms were used in this study. There were 105 clinical patients undergoing polysomnography for suspected OSA. We sampled the electrocardiogram (ECG) from wakefulness, stage 2, and REM sleep and analyzed for frequency domain HRV. Sampled epochs were free of apnea and arousals. Heart rate variability decreased with age. Total frequency variability (TF) and low frequency variability (LF) in wakefulness and REM sleep increased as apnea severity increased. Measures of TF, LF, and the LF/HF ratio were greatest in REM sleep. There was less LF and TF in Stage REM sleep in patients with higher BMI. In conclusion, the decrease in HRV with aging is a robust finding that occurs even in a clinical sleep apnea population. However, apnea does not mimic aging effects on the heart because HRV increased as apnea severity increased. The decrease in HRV during REM sleep in the obese apnea patients suggests the possibility of an autonomic dysfunction in this subgroup.