Chronic obstructive pulmonary disease (COPD) patients present functional and structural changes of the respiratory system that have a profound influence on cardiac autonomic dysfunction. To analyse heart rate variability in COPD patients under stable condition and during acute exacerbation episodes (AECOPD). Twenty three severe COPD male patients, 69.6 ± 7.3 years, in stable condition were followed up for two years. Home visits were carried out by a nurse every month, and home or hospital visits were arranged on demand. Every three months an ECG, oxygen saturation and spirometric recording was obtained for each patient. If the patient presented AECOPD compatible clinical data the same measurements were performed before any change of treatment. Spectral parameters of heart rate variability in time and frequency domains were obtained from ECG. The time evolution of power in low frequency (LF) and high frequency (HF) bands were obtained from the spectrogram. In addition, we calculated the LF/HF ratio and total heart rate variability power (POW). We analysed 154 patient-visit records during the follow up, pertaining to 23 patients and 8 controls; 19 of the patients had experienced at least one AECOPD. Stable COPD patients had higher HF values than control subjects. No significant differences were found in LF, LF/HF ratio or POW variables. AECOPD patients had higher LF, HF and POW than the stable COPD and control groups. AECOPD patients exhibited signs of increased autonomic activity compared with stable COPD.