With the development of three-dimensional techniques for imaging, such as computed tomography and magnetic resonance imaging, it is now possible to demonstrate the precise sinusal origin and epicardial course of the coronary arteries with just as much accuracy as can be achieved by the morphologist holding the heart in his or her hands. At present, however, there is no universally accepted convention for categorising the various patterns found when the heart is congenitally malformed. In this review, we show how, to provide such a convention, it is necessary to take note not only of the sinusal origin of the three major coronary arteries, but also the relationship of the aortic root relative to the cardiac base. We summarise the evidence showing how the proximal portions of the developing coronary arteries grow into the aortic valvar sinuses subsequent to the separation of the aortic root from the subpulmonary infundibulum. We also discuss the evidence showing that the subpulmonary myocardium is impervious to the passage of epicardial coronary arteries, and suggest that the process of septation itself plays an integral role in guiding the arteries into the two aortic sinuses that are adjacent to the pulmonary root. We then show how marriage of convenience between the epicardial coronary arteries and the aortic valvar sinuses provides a good explanation for the known variations found in the setting of transposition. We point out that it is the absence of septation that likely governs the patterns seen in the setting of a common arterial trunk.