BACKGROUND: Rhythm disturbances are frequent after Fontan operations. Arrhythmias related to reduced heart rate variability (HRV) have been described in various cardiovascular diseases. METHODS: We attempted to investigate HRV in 12 patients who underwent Fontan operation (age 11.4 +/- 3 years). Results were compared to a control group of 13 children matched for age, sex and heart rate (10.4 +/- 3 years). All patients underwent 24-hour Holter monitoring. The following time domain indexes were calculated: mean duration of RR intervals, standard deviation of all RR intervals (SD), square root of the mean squared differences of successive RR intervals (r-MSSD), percentage of differences between adjacent RR intervals > 50 msec (pNN50). The following frequency domain indexes were calculated: total power (TP), low frequency (LF), high frequency (HF), LF/HF ratio. RESULTS: The following indexes were significantly reduced in Fontan patients: SD (p < 0.0001), r-MSSD (p < 0.0001), pNN50 (p = 0.0002), TP (p < 0.0001), LF (p < 0.0001), HF (p = 0.0001). LF/HF increased significantly (p = 0.04). No differences were detected according to the type of operation (cavopulmonary connection vs atriopulmonary connection) or clinical status. CONCLUSIONS: Patients with Fontan circulation had a significantly reduced HRV and particularly abnormal sympatho-vagal balance. Surgery on the caval veins and the atria alters the intracardiac ganglia that are abundant at the cavo-atrial junction and in the myocardium of the right atrium. Abnormalities of HRV in Fontan patients may act as a co-factor in the initiation of arrhythmia in these patients.