Chronic obstructive pulmonary disease (COPD) is associated to cardiovascular morbidity and mortality, and abnormalities of the autonomic nervous system have been described in subjects with severe disease. We studied heart rate variability (HRV) in COPD patients at rest and during the 6-minute Walk Test (6mWT) and the association with lung function impairment taking into account systemic inflammation. Thirty outpatients with stable COPD underwent lung function measurements, blood gas analysis, ECG Holter and transcutaneous pulse oximetry during 6mWT and then they were classified by BODE index. Also C-reactive protein (CRP) was measured. At rest, we observed a significant reduction of HRV for increasing BODE index. During the 6mWT, HRV tended to decrease in BODE 1 subjects whereas an increase was observed in BODE 2 and BODE 3-4 subjects. Subjects with elevated CRP values had a significant reduction in Standard Deviation of all normal RR intervals at rest (SDNN: p = 0.013), Total Power (TFA: p = 0.04) and Very Low Frequency band (VLF: p = 0.041). At rest, subjects with Inspiratory Capacity-to-Total Lung Capacity ratio (IC/TLC) < 36% had a significant reduced SDNN (p = 0.004), TFA (p = 0.001), VLF (p = 0.001), Low Frequency band (p = 0.007). During 6mWT, changes of HRV parameters were significantly related to airflow obstruction and static hyperinflation indices. At rest and during submaximal exercise, COPD patients with moderate and severe disease had an abnormal cardiac autonomic modulation which was related to both systemic inflammation and lung function impairment.