To validate the use of particle traces derived from four-dimensional (4D) flow magnetic resonance (MR) imaging to quantify in vivo the caval flow contribution to the pulmonary arteries (PAs) in patients who had been treated with the Fontan procedure. The institutional review boards approved this study, and informed consent was obtained. Twelve healthy volunteers and 10 patients with Fontan circulation were evaluated. The particle trace method consists of creating a region of interest (ROI) on a blood vessel, which is used to emit particles with a temporal resolution of approximately 40 msec. The flow distribution, as a percentage, is then estimated by counting the particles arriving to different ROIs. To validate this method, two independent observers used particle traces to calculate the flow contribution of the PA to its branches in volunteers and compared it with the contribution estimated by measuring net forward flow volume (reference method). After the method was validated, caval flow contributions were quantified in patients. Statistical analysis was performed with nonparametric tests and Bland-Altman plots. P < .05 was considered to indicate a significant difference. Estimation of flow contributions by using particle traces was equivalent to estimation by using the reference method. Mean flow contribution of the PA to the right PA in volunteers was 54% ± 3 (standard deviation) with the reference method versus 54% ± 3 with the particle trace method for observer 1 (P = .4) and 54% ± 4 versus 54% ± 4 for observer 2 (P = .6). In patients with Fontan circulation, 87% ± 13 of the superior vena cava blood flowed to the right PA (range, 63%-100%), whereas 55% ± 19 of the inferior vena cava blood flowed to the left PA (range, 22%-82%). Particle traces derived from 4D flow MR imaging enable in vivo quantification of the caval flow distribution to the PAs in patients with Fontan circulation. This method might allow the identification of patients at risk of developing complications secondary to uneven flow distribution. http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.12120778/-/DC1.