Background and purpose <p>Variations of pulmonary arteries’ diameter and morphology are commonly encountered in different congenital heart diseases (CHD). They can have a profound impact on differential pulmonary flow (DPF). Abnormal DPF means unbalanced flow between both lungs, which can occur with various CHDs. This study aims to answer whether a significant difference in the differential pulmonary flow (SDDPF) is correlated with the complex morphometrics of the pulmonary arteries as an independent risk factor from the caliber.</p> Patients and methods <p>A retrospective study involved 152 patients who underwent cardiac magnetic resonance (CMR), including phase-contrast MRI (PC-MRI) of the main, right, and left pulmonary arteries (PAs). Evaluation of the caliber and morphology of the PAs, as well as the presence or absence of SDDPF through PC-MR, was done. Correlation between the discrepancy in pulmonary branch diameter (DPBD), major diagnosis, right ventricle (RV) size, function, pulmonary regurgitation (PR), and pulmonary artery morphology (PAM) versus SDDPF was evaluated.</p> Results <p>Forty patients had one or more morphologic patterns of concern. The most prevalent pattern among the patients with peculiar pulmonary artery morphology was left pulmonary artery (LPA) kink (57.5%). The SDDPF was observed more frequently in the group with peculiar PAM compared to the other group without this peculiar morphology (<i>P</i>-value = 0.000003).</p> Conclusions <p>The morphology of the pulmonary arteries (PAs) is a critical determinant of differential pulmonary blood flow, independent of their diameters. Among the various morphological patterns observed, the kink in the LPA is particularly prevalent and plays a consequential role in the discrepancies noted in pulmonary perfusion.</p>