Hypertrophic cardiomyopathy (HCM) is the most common cardiovascular genetic disorder, and can result in heart failure and sudden death in the young. No mutation is identified in up to 50% of cases of HCM following comprehensive analysis of known causal genes, however standard methods overlook large deletions and duplications. The multiple ligation-dependent probe amplification method was used to screen for large deletions and duplications in the myosin-binding protein-C (MYBPC3) and cardiac troponin T (TNNT2) genes in patients with HCM. One novel 3 base pair deletion was identified in MYBPC3 in a severely affected patient; however this change was also found in an unaffected relative. No alterations in the TNNT2 gene were identified. In conclusion, large deletions and duplications do not appear to play a major role in the pathogenesis of HCM.