Hypertrophic cardiomyopathy (HCM) is a complex heart disease with various physiopathological, morphological, functional, and clinical features. In this disease, HCM is known to be an autosomal genetic disease in more than half of the cases. Mutations in sarcomeric genes are thought to play an important role in the pathogenesis of the disease. Modifying genes and environmental factors also together affect the phenotypic expression and severity of HCM. The phenotypic expression of HCM is determined by causal sarcomeric gene mutations and the regulatory genetic basis of genes. HCM, a multi-factorial disease, involves the effects of many environmental gene modifiers and the sarcomeric/cytoskeletal genes. The single nucleotide polymorphisms occurring in the human genome differ in terms of susceptibility to disease in various populations. Therefore, the determination of genetic polymorphisms involved in the development of HCM disease is very important for the diagnosis of the disease.