OBJECTIVE: Patients with chronic obstructive pulmonary disease (COPD) appear to have impaired cardiac autonomic modulation with depressed heart rate variability (HRV). Pulmonary rehabilitation (PR) is recommended as an integral part of the management. However, the effect of PR on HRV at peak exercise remains unclear. METHODS: Sixty-four patients with COPD participated in a 12-week, 2 sessions-per-week, hospital-based PR program. Baseline and post-PR status were evaluated by spirometry, HRV, health-related quality of life (HRQL, St. George\'s Respiratory Questionnaire, SGRQ), cardiopulmonary exercise test, respiratory muscle strength, and dyspnea Borg\'s scale. RESULTS: After PR, there were significant improvements in the time and frequency domains of HRV with increased standard deviation of the normal R-R intervals, difference between adjacent normal R-R intervals within a given time minus one, high-frequency and decreased low-frequency, as well as concurrent improvements in HRQL, exercise capacity, dyspnea score, and respiratory muscle strength (all p < 0.05). CONCLUSIONS: PR results in significant improvements in autonomic function, with concurrent improvements in HRQL and exercise capacity.