Background: A protective effect of exercise in preventing sudden cardiac death is supported by studies in healthy populations as well as in patients with cardiac disease. The mechanisms involved in this protective effect are unknown. Hypothesis: We hypothesized that exercise conditioning would beneficially alter autonomic nervous system tone, measured by heart rate variability. Methods: We prospectively studied 20 cardiac patients enrolled in a Phase 2 12-week cardiac rehabilitation program following a recent cardiac event. The patients underwent 24 h Holter monitoring at program entry and 12 weeks later. Heart rate variability analysis was assessed for both time domain and spectral analysis. Results: The group demonstrated a modest mean conditioning effect, indicated by an average reduction in resting heart rate from 81 +/- 16 to 75 +/- 12 beats/min (p = 0.03), and an increase in training METS from 3.1 +/- 0.4 to 3.3 +/- 1.1 (p < 0.0001). Overall, 15 of 20 (75%) patients demonstrated increased total and high-frequency power, and mean high-frequency power was significantly increased (3.9 +/- 1.4 vs. 4.3 +/- 1.0 ln, p = 0.05). When stratified according to the magnitude of exercise conditioning, patients achieving an increase of >1.5 training METS demonstrated significant increases in SDNN, SDANN index, SDNN index, pNN50, total power, and high-frequency power (all p < 0.05) (see text for explanation of abbreviations). Conclusions: Exercise conditioning improves heart rate variability in cardiac patients, particularly in patients who achieve a threshold of > 1.5 training METS increase over a 12-week period. These study results are supportive of the concept that exercise training lowers the risk of sudden cardiac death via increased vagal tone, which likely beneficially alters ventricular fibrillatory and ischemic thresholds.