BACKGROUND: In coronary artery disease (CAD) and following myocardial infarction (MI), activity of the autonomic nervous system is altered. Reduced heart rate variability (HRV) is a risk factor for future cardiac event. Studies reporting changes in HRV post-cardiac rehabilitation (CR) are heterogeneous, due possibly to varied data collection and analysis protocols. AIM: To evaluate changes in spectral measures of HRV derived from 5-minute ECG recordings in patients completing an 8 weeks CR programme. METHODS: Thirty-eight patients (21 males, 17 females, aged 65.6 +/- 11.6 years) underwent 5 minutes, supine ECG recordings and standard physiological and psychological assessment pre- and post-CR. A further 23 patients (14 males, 9 females aged 64.9 +/- 9 years) acted as controls. Outcome measures were: low frequency power, (LF, 0.04-0.15 Hz) high frequency power (HF, 0.15-0.40 Hz), LF:HF ratio and mean RR interval. Change was assessed by ANCOVA and paired t-tests. RESULTS: When compared with the CT group, the CR group showed significant increases in: SDNN (Delta +6 ms, CR vs. 0 ms CT), HFln (Delta 0.4 log units CR vs. 0 log units CT), LFln (Delta +0.6 log units CR, vs. +0.1 log units CT) and RR interval (Delta +30 ms, CR vs. -28 ms CT). CONCLUSIONS: This is the first study to show significant increases in raw LF and HF power derived from short-term ECG recordings in CR patients. These measures are risk factors for future cardiac event. As CR is associated with increases in these measures it may be viewed as an effective therapy capable of bringing about favourable alterations in autonomic control.