Hypertrophic cardiomyopathy is a heterogeneous clinical syndrome with a wide spectrum of pathophysiologic consequences. Most cases are inherited and caused by sarcomeric protein gene mutations, although phenocopies are often encountered. Genomic research and family studies have improved our recognition of the disease and understanding of its natural history; however, tenuous links exist between genotype and phenotype and thus far have done little to alter clinical management. Surgery and, more recently, implantable cardiac defibrillators have had an impact on sudden cardiac death rates, with improved short- and medium-term survival. Therefore, managing heart failure has become increasingly challenging. Although heart failure due to fibrosis and a progressive loss of contractile function is common, treatment remains largely empiric. Case series and animal studies suggest that biventricular pacing and renin-angiotensin-aldosterone system modifiers may be useful in some patients, but there is a need for large prospective randomized controlled trials to study these and other treatments. Risk stratification and eligibility for sports participation remain hot topics, but one of the greatest challenges is the management of a growing cohort of asymptomatic gene carriers identified during family screening. Ultimately, major advances in treatment and disease prevention will come from a better understanding of the genomic, proteomic, and metabolomic profiles of individual patients.