Hypertrophic cardiomyopathy is a relatively common genetic disease, affecting one person per 500 in the general population, and is clinically defined by the presence of unexplained left ventricular hypertrophy. Although recognized as the most common cause of sudden death in the young (especially in athletes), the cardiac expression of the disease is highly variable with respect to age at onset, degree of symptoms and risk of cardiac death. As a consequence, therapeutic strategies are diverse and must be adapted to the specific features of an individual. Recently, the molecular bases of the disease have been unraveled with the identification of a large number of mutations in genes encoding sarcomeric proteins. This review focuses on the impact of the molecular data on the understanding of the disease, and considers the emerging issues regarding the impact of molecular testing on the management of patients (or relatives) in clinical practice.