Background: Heart rate recovery (HRR) as a function of vagal reactivation, which is an independent risk predictor for cardiovascular disease and mortality, is strongly associated with metabolic syndrome. Methods: Middle-aged obese men (metabolic syndrome, n = 20; non-metabolic syndrome, n = 22) classified on the basis of Adult Treatment Panel III criteria were investigated in this study. Postexercise HRR and the HRR decay constant following a symptom-limited bicycle exercise test were evaluated before and after a 12-week exercise training program (60-70% of maximal heart rate; 60 minutes per day; 3 days per week). Results: Although the peak HR remained unchanged, HR at anaerobic threshold significantly decreased for both groups after exercise training; HR at rest was significantly decreased in the metabolic syndrome group after training (P < 0.05). HRR significantly improved in the metabolic syndrome group (-26.1 +/- 3.6 beats/minute vs. -33.5 +/- 3.8 beats/minute, at 1 minute; -39.9 +/- 4.9 beats/minute vs. -49.5 +/- 4.9 beats/minute, at 2 minute, P < 0.05) with no change for the non-metabolic syndrome group (P > 0.05). HRR decay constant values showed signifi cant improvement in the metabolic syndrome group (0.31 +/- 0.02%/second vs. 0.35 +/- 0.02%/second, P = 0.038) after exercise training but not the non-metabolic syndrome group (P > 0.05). Conclusions: This study demonstrated that moderate-intensity physical training without caloric restrictions improves HRR in obese men with metabolic syndrome, possibly due to a reduction in the resting HR. Therefore, weight loss-induced exercise training would help in improving the resting HR, and the responsiveness of the autonomic nervous system in obese men with metabolic syndrome.