Outflow tract defects, including cardiac neural crest defects (so-called conotruncal defects) and transposition of the great arteries, are due to an abnormal rotation of the outflow tract during cardiac development. Coronary orifices are often abnormal in outflow tract defects, particularly in common arterial trunk (CAT). A recent study indicates that abnormal coronary artery pattern in a mouse model with common arterial outlet (Tbx1−/− mouse mutant) could be due to a reduced and malpositioned subpulmonary coronary-refractory myocardial domain. The aim of our study was to demonstrate the relation between coronary orifices pattern in outflow tract defects in human and the abnormal embryonic rotation of the outflow tract. We analyzed 101 heart specimens with outflow tract defects: 46 CAT, 15 tetralogy of Fallot (TOF), 29 TOF with pulmonary atresia (TOF-PA), 11 double-outlet right ventricle with subaortic ventricular septal defect (DORV) and 17 controls. The position of left and right coronary orifices (LCO, RCO) was measured in degrees on the aortic/truncal circumference. The anterior angle between LCO and RCO (α) was calculated. The LCO was more posterior in TOF (31 °), TOF-PA (47 °), DORV (44 °), CAT (63 °), compared with controls (0 °, P < 0.05), and more posterior in CAT than in other outflow tract defects (P < 0.05). The RCO was more anterior in TOF (242 °), TOF-PA (245 °) and DORV (271 °) than in controls (213 °, P < 0.05), but not in CAT (195 °). The α angle was similar in TOF, TOF-PA, DORV and controls (149 °, 162 °, 133 °, 147 °), but significantly larger in CAT (229 °, P < 0.0001). In all outflow tract defects but CAT, the displacement of LCO (anterior) and RCO (posterior), while the α angle remains constant, might be due to incomplete rotation of the myocardium at the base of the outflow tract, leading to an abnormally positioned subpulmonary coronary-refractory myocardial domain. The larger α angle in CAT could reflect its dual identity, aortic and pulmonary.