[Purpose] This study evaluated the effect of Bilevel Positive Airway (BiPAP) on the autonomic control of heart rate, assessed by heart rate variability (HRV), in patients hospitalized with decompensated heart failure. [Subjects and Methods] This prospective cross-sectional study included 20 subjects (age: 69+/-8 years, 12 male, left ventricular ejection fraction: 36 +/-8%) diagnosed with heart failure who were admitted to a semi-intensive care unit with acute decompensation. Date was collected for HRV analysis during: 10 minutes spontaneous breathing in the resting supine position; 30 minutes breathing with BiPAP application (inspiratory pressure = 20 cmH2O and expiratory pressure = 10 cmH2O); and 10 minutes immediately after removal of BiPAP, during the return to spontaneous breathing. [Results] Significantly higher values for indices representative of increased parasympathetic activity were found in the time and frequency domains as well as in nonlinear Poincare analysis during and after BiPAP in comparison to baseline. Linear HRV analysis: standard deviation of the average of all R-R intervals in milliseconds = 30.99+/-4.4 pre, 40.3+/-6.2 during, and 53.3+/-12.5 post BiPAP. Non-linear HRV analysis: standard deviations parallel in milliseconds = 8.31+/-4.3 pre, 12.9+/-5.8 during, and 22.8 +/-6.3 post BiPAP. [Conclusion] The present findings demonstrate that BiPAP enhances vagal tone in patients with heart failure, which is beneficial for patients suffering from acute decompensation.