The introduction of molecular biology in Cardiology opened a new era, in which the collaboration between geneticists, molecular biologists and cardiologists will allow the clinical application of Molecular Cardiology. In this review the new advances in the diagnosis and prognostic evaluation of patients with Hypertrophic Cardiomyopathy at the molecular level are discussed. We also present a summary of our current knowledge on the genetic bases and molecular mechanisms of this disease. Finally, some possibilities of the future clinical application of the data obtained by Genetic and Molecular Biology are shown. The Molecular Biology of Hypertrophic Cardiomyopathy expanded our horizons beyond the morphologic definitions, exposing the limitations of traditional concepts. However, we should not forget the potential drawbacks of these genetic tests, in order to anticipate and prevent the problems associated with their performance.