Congenital heart defects affect the efficiency and functionality of the heart, and autonomic control of heart rate and of circulation can display a pathologic behavior in order to compensate for the hemodynamic alterations due to disease. While previous works have investigated heart rate variability (HRV) in specific pathologies, e.g. tetralogy of Fallot, the goal of this study was to assess HRV in children with a congenital heart malformation taking into account the effects of cyanotic and acyanotic defects, and comparing pathologic children with age matched controls. HRV, approximate entropy (ApEn) and sample entropy (SampEn) were calculated to discuss the dynamics and complexity of heart rhythms, and to evaluate the potential impairment of control mechanisms. Analyses showed that low frequency (LF) power and total power of HRV were significantly higher in children with a condition than in healthy controls, independently of cyanosis. Non linear indices were also significantly higher in pathologic subjects. Significant differences in LF, total power, ApEn and SampEn were found among cyanotic, acyanotic and healthy children. These results suggested that children with a congenital heart condition display more complex HRV and sympathetic overactivity, which may be aimed at compensating for hemodynamic alterations. Further studies should investigate whether corrective surgery and rehabilitation can improve HRV and restore its physiological features.