Background In hearts with congenitally corrected transposition of the great arteries, the atrial and ventricular septums are usually malaligned. This is associated with an abnormal location of the atrioventricular conduction system. However, well-aligned septums and normally positioned atrioventricular conduction tissues have been found in a few cases, some of which also happened to have a small or atretic pulmonary trunk. Our aim was to determine whether septal alignment could be predicted on the basis of the size of the pulmonary trunk. Potentially this could provide a guide to the disposition of the atrioventricular conduction tissues. Methods We examined 14 hearts. In all cases there was usual atrial arrangement. We carried out histologic examination of the sites of the atrioventricular conduction tissues in 1 heart. Results We found a statistically significant correlation between the size of the pulmonary trunk and the degree of septal malalignment. In the presence of a small or atretic pulmonary trunk, the septums were well aligned. Our histologic study of one such specimen revealed dual atrioventricular nodes connecting to a sling of conduction tissue. This suggests that presence of a postero-inferiorly situated atrioventricular conduction bundle in addition to an anteriorly located bundle may be anticipated when the septums are well aligned. Conclusions The presence of a small or atretic pulmonary trunk in congenitally corrected transposition of the great arteries is associated with good septal alignment. This should alert the surgeon to the possibility of a slinglike arrangement of the atrioventricular conduction system.