BACKGROUND: Analysis of heart rate variability (HRV) provides a noninvasive index of autonomic nervous system activity. HRV has shown to be reduced in congestive heart failure and in children with congenital heart disease (CHD). Beta-blockers improve HRV in adults with congestive heart failure, but this improvement remains to be demonstrated in children. MATERIAL/METHODS: HRV was analysed in 14 infants with severe heart failure due to CHD who received a \'standard\' therapy with digoxin and diuretics (\'Digoxin/Diuretics\' group) and in 9 of these patients with an additional propranolol therapy (\'Propranolol\' group) 17 days later on average and compared with HRV of 70 healthy infants (\'Healthy Control\'). RESULTS: Comparing the \'Digoxin/Diuretics\' group versus \'Healthy Control\', we found significantly reduced HRV in the time domain and the frequency domain, that could be abolished in the \'Propranolol\' group. None of the HRV parameter were significantly related to age or any hemodynamic parameter but inversely related to ejection fractions within the normal range (pNN50: r= -0.58, p=0.004; rMSSD: r= -0.42; p=0.049). HRV measurements (SDNN, r= -0.48) and plasma norepinephrine levels (r=0.7) were significantly related to clinical symptoms of heart failure, measured by the Ross Score. CONCLUSIONS: HRV represents a noninvasive parameter that is reduced in infants with congenital heart disease depending on the severity of heart failure but not on hemodynamic disturbances. Propranolol but not digoxin therapy effectively reduced the supposed autonomic imbalance in infants with severe heart failure due to CHD.