Background: Hypertrophic Cardiomyopathy (HCM) is a complex myocardial disorder with a recognized geneticheterogeneity. The elevated number of genes and mutations involved in HCM limits a gene-based diagnosis thatshould be considered of most importance for basic research and clinical medicine.Methodology: In this report, we evaluated High Resolution Melting (HRM) robustness, regarding HCM genetictesting, by means of analyzing 28 HCM-associated genes, including the most frequent 4 HCM-associated sarcomeregenes, as well as 24 genes with lower reported HCM-phenotype association. We analyzed 80 Portugueseindividuals with clinical phenotype of HCM allowing simultaneously a better characterization of this disease in thePortuguese population.Results: HRM technology allowed us to identify 60 mutated alleles in 72 HCM patients: 49 missense mutations, 3nonsense mutations, one 1-bp deletion, one 5-bp deletion, one in frame 3-bp deletion, one insertion/deletion, 3splice mutations, one 5'UTR mutation in MYH7, MYBPC3, TNNT2, TNNI3, CSRP3, MYH6 and MYL2 genes. Significantly22 are novel gene mutations.Conclusions: HRM was proven to be a technique with high sensitivity and a low false positive ratio allowing arapid, innovative and low cost genotyping of HCM. In a short return, HRM as a gene scanning technique could bea cost-effective gene-based diagnosis for an accurate HCM genetic diagnosis and hopefully providing new insightsinto genotype/phenotype correlations.