Objective: The aim of this case-controlled, cross-sectional study is to investigate the tendency towards arrhythmia using noninvasive arrhythmia markers (QT dispersion and heart rate variability) in children with Eisenmenger syndrome. Methods: We studied 23 patients, whose pulmonary-to-systemic resistance ratio was calculated to be greater than 0.75, and who were diagnosed as Eisenmenger syndrome between 1990 and 2001. Twenty healthy children were studied as the control group. Electrocardiographic recordings with calculation of QT dispersion, Holter monitoring, echocardiographic studies and heart rate variability (HRV) analysis were performed in both groups. Catheterization records were analyzed in all the patients. Results: QT and QTc dispersion were higher (p=0.007 and p=0.006, respectively) and PR interval was longer (p=0.009) in the patients with Eisenmenger syndrome, than those in the control group. In addition, low frequency component, high frequency component, very low frequency component, and total power, obtained from HRV analysis were significantly lower in the patients with Eisenmenger syndrome (p=0.001, p=0.006, p=0.009 and p=0.011, respectively). Evaluation of Holter recordings revealed pathologic findings in 21.7% of the patients with Eisenmenger syndrome. Pulmonary-to-systemic resistance ratio of the patients with pathologic Holter findings were higher than in the patients with normal Holter recordings (p=0.011). It was also shown that there was a positive correlation between OT dispersion and pulmonary-to-systemic resistance ratio (p=0.048, r=0.416) and between QT dispersion and PR interval (p=0.009, r=0.532) in the patients with Eisenmenger syndrome. Conclusion: Dispersion of repolarization, being associated with high pulmonary-to-systemic resistance ratio, is increased and autonomic modulation of heart rate is impaired in patients with Eisenmenger syndrome. These findings suggest that arrhythmia risk for patients with Eisenmenger syndrome is higher than in normal controls.