We summarize recent advances in the clinical genetics of hypercholesterolemia, hypertrophic cardiomyopathy (HCM), and lethal arrhythmia, all of which are monogenic cardiovascular diseases being essential to understanding the heart and circulatory pathophysiology. Among the issues of hypercholesterolemia which play a pivotal role in development of vascular damages, familial hypercholesterolemia is the common genetic cardiovascular disease; in addition to identifying the gene mutation coding low-density lipoprotein receptor, lipid kinetics in autosomal recessive hypercholesterolemia as well as in proprotein convertase subtilisin/kexin 9 gene mutation were recently demonstrated. As for HCM, some gene mutations were identified to correlate with clinical manifestations. Additionally, a gene polymorphism of the renin-angiotensin system in development of heart failure was identified as a modifier gene. The lethal arrhythmias such as sudden death syndromes, QT prolongation, and Brugada syndrome were found to exhibit gene mutation coding potassium and/or sodium ion channels. Interestingly, functional analysis of these gene mutations helped to identify the role of each gene mutation in developing these cardiovascular disorders. We suggest considering the genetic mechanisms of cardiovascular diseases associated with hyperlipidemia, myocardial hypertrophy, or lethal arrhythmia in terms of not only clinical diagnosis but also understanding pathophysiology of each disease with therapeutic aspects.