Although the normal aortic and pulmonary roots have some features in common, they also exhibit important anatomical and functional differences. These differences increase when compared with surgically created neo-aortic roots in individuals with congenitally malformed hearts, with the substrates initially having been either a pulmonary root originating from the right or left ventricle, or a truncal root with variable ventricular origin. With the increasing application and success of these surgeries, our attention has now turned toward understanding late outcomes. Subsequent dilation, usually producing neo-aortic valvar regurgitation, is the most common cause of reoperation in any procedure involving a neo-aortic root. In this review, we describe and compare the detailed anatomy of the normal aortic, pulmonary, and common truncal roots, comparing them with the changes observed in the neo-aortic root following various common surgeries providing biventricular repair for congenital cardiac malformations. We focus on the dilated and dysfunctional neo-aortic root, assessing how the anatomical information relates to contemporary surgical techniques. Furthermore, we aim to review risk factors as they relate to the adverse anatomical features which become evident when the new root is dysfunctional, hoping to provide surgical insight toward optimizing its function and durability.