Congenitally diseased valves are relatively frequent causes of significant morbidity and mortality. Pathology descriptions of such valves have primarily focused on gross structural features including the number of leaflets or commissures (bicuspid/bicommissural valve) and alterations in the contour, thickness and consistency of the leaflets (dysplastic valve). Functional correlates of these pathologic alterations are valvar stenosis, insufficiency or both. Further characterization of the microstructural abnormalities seen in these malformed valves may not only provide insight into the correlation of distinct pathologies with their respective pathogenesis and clinical sequelae, but also may prove pivotal in uncovering new avenues for therapeutic interventions and prevention regimens. This review summarizes microstructural findings in congenital semilunar valve disease (CSVD) and discusses their relevance in light of recent advances in knowledge of normal valve microstructure, biology, and function. Specifically, the biological and mechanical roles of various matrix components and their interactions are discussed in the context of CSVD. Indeed, recent research in normal valves adds significant insight into CSVD, and raises many hypotheses that will need to be addressed by future studies.