The effect of positive airway pressure treatments in different modalities on the cardiovascular consequences of the disease in sleep apnea patients is still unclear. We aimed to compare auto-titrating positive airway pressure (APAP) and conventional continuous positive airway pressure (CPAP) in terms of improving heart rate variability (HRV) in obstructive sleep apnea patients. This was a prospective study done in a tertiary research hospital. All patients underwent a manual CPAP titration procedure to determine the optimal pressure that abolishes abnormal respiratory events. Then patients underwent two treatment nights, one under APAP mode and one under conventional CPAP mode with a 1-week interval. Forty newly diagnosed obstructive sleep apnea patients were enrolled in the study. We compared heart rate variability analysis parameters between the APAP night and the CPAP night. This final analysis included the data of 28 patients (M/F: 22/6; mean age = 46 +/- 10 years). Sleep characteristics were comparable between the two treatment nights, whereas all-night time domains of HRV analysis such as HF, nuLF, and LF/HF were different between APAP and CPAP nights (2.93 +/- 0.31 vs. 3.01 +/- 0.31; P = 0.041; 0.75 +/- 0.13 vs. 0.71 +/- 0.14; P = 0.027; and 4.37 +/- 3.24 vs. 3.56 +/- 2.07; P = 0.023, respectively). HRV analysis for individual sleep stages showed that Stage 2 LF, nuLF, nuHF, LF/HF parameters entirely improved under CPAP treatment whereas APAP treatment resulted in nonsignificant changes. These results suggest that despite comparable improvement in abnormal respiratory events with APAP or CPAP treatments, CPAP may be superior to APAP in terms of correcting cardiovascular alterations in sleep apnea patients.