Background: The assessment of Fontan circuit's flow is traditionally evaluated by multiple through-plane phasecontrast MRI acquisitions (2D flow), while recently, a single volumetric 4D-flow MRI acquisition is emerging as a comprehensive tool for the hemodynamic evaluation in congenital heart diseases. Purpose: To compare 2D and 4D-flow MRI measurements in patients after Fontan palliation and to evaluate parameters affecting potential disagreement. Methods: 39 patients after Fontan palliation (23 males, age 22 ± 11 years) who underwent cardiac MRI with 2D and 4D-flow MRI acquisition were included in the study. In all patients, blood flow quantification in the Fontan circuit and aorta by 2D flow and by 4D flow MRI acquisition blinding to the 2D results was performed. The agreement between 2D and 4D-flow MRI was calculated as the intraclass correlation coefficient (ICC). The mean absolute differences between 4D and 2D flows were analyzed using linear regression models. Results: 4D-flow MRI acquisition time was slightly lower than 2D (7.6 ± 1.8 min vs. 9.4 ± 3.3 min, p = 0.03). Flow was slightly predominant in the right pulmonary artery (58% of total pulmonary flow). Conduit/tunnel-pulmonary arteries flow accounted for 60% of the Fontan circuit. Agreement between 2D and 4D was overall goodto-excellent from ICC: 0.817 95% CI: 0.637-0.907 to 0.932 95% CI: 0.866-0.965. There was no significant influence of evaluated parameters on the agreement on 4D and 2D flow. Conclusions: 4D-flow MRI represents a valid tool in Fontan's flow quantification. Further larger studies are needed to confirm our results and to evaluate the impact of advanced 4D-flow MRI parameters on the prognostic stratification in patients after Fontan palliation.