The normal heart possesses two ventriculo-arterial junctions – one for the aortic valve, and the other for the pulmonary valve. In the normal heart, these pulmonary and aortic roots are discrete and separate structures, the subpulmonary infundibulum being a free-standing muscular sleeve, separated by extracardiac space from the outflow tract of the left ventricle. When considering the congenital malformations that can distort these outflow tracts, it is conventional to categorise them as existing at subvalvar, valvar, and supravalvar levels. Such an approach, however, ignores the fact the valvar leaflets themselves extend through a significant length of the outflow tracts, with so-called supravalvar stenosis almost always involving the sinutubular junction, this being an integral part of the mechanism that normally ensures competent valvar closure. When considering the lesions that involve abnormally structured outflow tracts, these are best analysed by recognising the different features of the ventriculo-arterial junctions, namely the way the arterial trunks are joined to their underlying ventricles, the interrelationships of the trunks one to the other, and the arrangement of the supporting ventricular structures. In this review, we will show how knowledge of the arrangement of the normal junctions provides the necessary scaffold for logical analysis of all the lesions that can afflict the outflow tracts, be they otherwise normally or abnormally structured.