In normal anatomy, the left pulmonary artery (LPA) is usually situated higher than the right pulmonary artery (RPA); however, transposition of the great arteries (TGA), the LPA is not always situated higher than the RPA. This study was performed to clarify the relative position of the RPA and the LPA in transposition of the great arteries (TGA) as well as the implications. We reviewed 101 angiograms of patients with TGA (age 4.1 ± 1.2 months). The width of the RPA, the LPA, and the pulmonary trunk (PT) were measured just before their first branch in the frontal view. They were classified into four groups according to the ratio between the RPA and the PT (RPA/PT). The initial courses of the LPA and the RPA were compared and defined according to their height in the frontal view, and the preferential flow (or not) to the RPA was recorded. The equation of hydrodynamics was applied to evaluate the bifurcation angle. Both PAs were the same size in all cases. Forty-eight patients (47.5 %) had a RPA/PT diameter ratio < 0.49. The LPA coursed higher than the RPA in the majority of cases (81 [80.2 %]); in a minority of cases the LPA and RPA were at the same level (6 [5.9 %]); and in some cases the RPA coursed higher than the LPA (14 [13.9 %]). Patients with a high degree of PA hypoplasia tended to have both PAs at the same level or a higher-positioned RPA. Autopsy (1 of 3 cases) showed a posterior ridge against the bronchus in the higher RPA. Hydrodynamic calculation showed that the greater the angle between the RPA/PT, the greater the preferential flow. Preferential flow to the RPA in TGA did not necessarily result in LPA hypoplasia before its first branch. Higher RPA position relative to the LPA was associated with greater flow in it against the posterior bronchus. This situation was more prevalent in patients with severe PA hypoplasia.