Bicuspid aortic valve (BAV) is the most common congenital abnormality of the human heart, affecting approximately 1-2% of the general population (Williams, 2006). It is widely accepted that BAV is a very heterogeneous disease and that the different phenotypes of BAV disease may be caused by unique pathogenetic mechanisms. Because the heterogeneous nature of BAV disease has been recognized by many researchers, attempts have been made to stratify the most common anatomic-clinical forms. The clinically observed linkage between specific BAV morphology and the associated lesions of the proximal aorta has recently led to several phenotypic classifications which incorporate both valve and proximal aortic anatomy. These different BAV phenotypes may be caused by unique pathogenetic mechanisms and may require different therapeutic approaches. The clarification of this phenomenon will undoubtedly affect the individual treatment strategy of BAV disease. In the face of these novel findings, this chapter deals with recent controversies in BAV disease.