Hypertrophic cardiomyopathy (HCM) is a relatively common genetic disease, generally with a benign prognosis. However sudden cardiac death may occur, sometimes as the first manifestation of the disease. More than two hundred different mutations have been described in HCM, in 12 different genes encoding sarcomere proteins. This genetic diversity is accompanied by considerable clinical variability and it is likely that phenotype is partially determined by genotype. In recent years it has been suggested that genetic defects could be the major markers of prognosis. Thus, some mutations would carry a good prognosis whereas others, so-called 'malignant' mutations, would be associated with premature sudden death. In a Portuguese population of 35 index patients with HCM the authors found considerable genetic heterogeneity: seven of the 12 mutations identified were de novo, each family having its own 'private' mutation. Moreover, in two unrelated families with the same mutation (I263T--exon 9, missense) in the beta-myosin heavy chain gene (MYH7), penetrance, clinical expression and prognosis were quite different, particularly regarding the occurrence of sudden cardiac death. In two other also unrelated families, in each index patient a different mutation was identified in the troponin I gene (TNNI3): A157V (missense), exon 7 and S199N (missense), exon 8. Phenotypic expression was different but both patients suffered sudden cardiac death (one survived). This suggests that mutations in this gene carry an adverse prognosis. In conclusion, the considerable genetic and clinical variability found in HCM hinders the interpretation of genotype-phenotype correlations, particularly since all the published data is based on small numbers of families.