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We compared the effects of 2‐month CPAP or exercise training (ET) therapies on the autonomic balance in moderate to severe obstructive sleep apnea (OSA) through heart rate variability (HRV) analysis. Thirty‐nine OSA patients were divided into CPAP (n = 18) and ET (n = 21) groups, being further split into hypertensive and non‐hypertensive subgroups. All patients were submitted to continuous ECG recordings for HRV analysis. Hemodynamic parameters were recorded by oscillometry. Excessive daytime sleepiness and sleep quality were assessed through the Epworth Sleepiness Scale and the Pittsburgh questionnaire, respectively. ET decreased systolic arterial pressure in hypertensive and non‐hypertensive participants when compared to baseline values, whereas diastolic arterial pressure was decreased only in non‐hypertensive ones. CPAP had no effect over hemodynamic parameters in either subgroup. ET significantly increased the HRV parameters SDNN and pNN50 in non‐hypertensive participants, while reducing the LF/HF ratio in both subgroups. CPAP significantly decreased SDNN in both subgroups. ET significantly decreased excessive daytime sleepiness in both subgroups, but did not affect sleep quality. CPAP significantly improved sleep quality in both subgroups, although global scores were still those of poor sleepers, while excessive daytime sleepiness was normalized only in hypertensive patients. In conclusion, while short‐term ET modulated different HRV parameters, leading to a predominant vagal tone in the cardiac sympathovagal balance and decreasing blood pressure in moderate to severe OSA, short‐term CPAP had next to no effect in these parameters. We believe ET should be considered as an adjunct interventional strategy in the conservative management of hypertensive or non‐hypertensive OSA patients.

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