OBJECTIVES: Patients with obstructive sleep apnea (OSA) experience sympathetic hyperactivation during sleep, which is associated with increased cardiovascular risk factors. However, the difference in cardiac autonomic activity in OSA patients according to position dependency has not been evaluated. This study aimed to evaluate the differences between positional OSA (pOSA) and nonpositional OSA (npOSA) using heart rate variability (HRV) analysis. METHODS: This was a single-center cross-sectional study. Twenty-eight patients with npOSA and 28 age-, sex-, and AHI-matched patients with pOSA underwent standard polysomnography. A five-minute R-R interval from stable waking conditions before bedtime was collected from each subject and analyzed for HRV. RESULTS: Patients with pOSA had lower body-mass index (BMI, 25.8 +/- 2.9 vs 28.9 +/- 3.7 kg/m(2), p = 0.001), shorter apnea duration (24.1 +/- 7.1 vs 30.3 +/- 12.7 s, p = 0.028) and higher minimum oxygen saturation (78.2 +/- 7.1 vs 71.5 +/- 11.4%, p = 0.011) than those with npOSA. HRV analysis showed higher parasympathetic activity in pOSA patients than in npOSA patients, including a higher square root of the mean of the sum of the squares of differences between adjacent NN intervals (RMSSD, 31.3 +/- 29.0 vs 18.6 +/- 9.2, p = 0.032), percentage of pairs of adjacent NN intervals that differ by more than 50 ms (pNN50%, 10.7 +/- 17.1 vs 3.3 +/- 6.5, p = 0.024), and high-frequency (HF) power (534.7 +/- 986.8 vs 146.7 +/- 150.5, p = 0.026). The group difference was insignificant after adjusting for age and BMI. The log-transformed supine/nonsupine AHI ratio was the sole independent predictor of HRV parameters. CONCLUSION: The waking HRV was higher in pOSA patients than in npOSA patients due to the lower BMI of pOSA patients. The difference was especially apparent in parasympathetic indices. Higher parasympathetic activity in pOSA may suggest a lower risk for cardiovascular morbidity and mortality.