We assessed heart rate (HR) recovery following peak exercise before and after a 12-week cardiac rehabilitation program in 14 children, 12.1+/-1.8 years of age, with repaired complex congenital heart disease (CHD; 11 with Fontan surgery) and impaired exercise performance. Exercise testing using bicycle ergometry was performed at baseline, after completion of the rehab program and 1.0+/-0.2 years after the baseline test. These data were compared to HR recovery in 15 controls (age, 12.7+/-2.4 years) with CHD (13 with Fontan surgery) with two serial exercise tests at an interval of 1.1+/- 0.3 years. There was no change in peak HR between the two serial tests in either group. Peak VO2 improved in the rehab group (26.3+/-9.6 ml/kg/min at baseline vs 30.9+/-9.6 ml/kg/min after rehab, p=0.01) but remained unchanged in controls on serial testing. One-minute HR recovery (in beats per minute) improved significantly following completion of the rehab program (27+/-15 at baseline vs 40+/-23 after rehab, p=0.01). Partial improvement in 1-minute HR recovery in the rehab group persisted 1 year later (1-minute HR recovery, 35+/-19; p=0.1 compared to baseline). There was no change in 1-minute HR recovery over time in the control group (37+/-16 vs 40+/-13, p = not significant). In conclusion, HR recovery following peak exercise improves in children with CHD after participation in a cardiac rehab program.