Background: Focusing on patients with arrhythmia, the aims of this study was to assess ventricular function in children using three-dimensional echocardiography (3D-ECHO) and to compare the results to those obtained with cardiac magnetic resonance (CMR). Methods: The study group consisted of 43 children in whom 3D-ECHO and CMR were performed. Twenty-five patients had a ventricular arrhythmia, 7 left ventricular cardiomyopathies, 9 proved to be healthy. In all children, 3D-ECHO (offline analysis) was used to assess ventricular ejection fraction (EF). The results were compared to CMR using the Bland-Altman analysis and linear regression. The Student paired T-test was used to compare of means between both modalities. Results: The relation between the results derived from both methods is linear (for left ventricle: estimated slope = 1.031, p < 0.0001, R-squared = 0.998; for right ventricle: estimated slope = 0.993, p < 0.0001, R-squared = 0.998). In spite of minimal mean differences between results for both ventricles and narrow 95% confidence intervals, the paired t-test proved those differences not to be significant (p > 0.05) for the right ventricle but statistically significant (p < 0.05) for the left ventricle, for which the left ventricular EF calculated in 3D-ECHO was systematically underestimated with a mean difference of-1.8% ± 2.6% (p < 0.0001). Conclusions: Three-dimensional echocardiography assessment of both left and right ventricular EF in children showed high significant correlation and agreement with CMR. 3D-ECHO could be a valuable tool in follow-up of children with arrhythmic disorders requiring regular assessment of ventricular function.