Familial hypertrophic cardiomyopathy (HCM) is a primary cardiomyopathy with an autosomal dominant pattern of inheritance. The disease bearing genes for HCM in HCM families have been identified as beta-myosin heavy chain, alpha-tropomyosin, cardiac troponin T (cTnT) and myosin binding protein-C genes. In the present study, we searched for the mutations in the cTnT gene in Japanese HCM patients. Single-strand conformation polymorphism gel analysis of polymerase chain reaction-amplified product was used to search for the mutations in the exons 8, 9 and 15 of the cTnT gene from 60 familial HCM patients. Clinical studies of the family members were performed and the incidence of sudden or disease-related deaths within the family was also examined. We have identified a novel missense mutation in exon 9 (Ala104Val) of the cTnT gene in a patient with familial HCM. Because the missense mutation was found at the residue conserved through chicken to humans and was not detected in the more than 50 normal controls, it was suggested that this missense mutation is the cause of HCM in this family. Although the affected family members presented moderate hypertrophy of the left ventricular wall, they were symptomatic and there was a high incidence of sudden death in her family members. Among Japanese patients with familial HCM, a novel missense mutation (Ala104Val) in the cTnT gene was identified. Familial HCM is genetically heterogeneous in Japanese HCM patients as observed in Caucasian kindreds. The disease in the kindred was severe and there was a high incidence of sudden or disease-related deaths in the kindred with this mutation.