Mitochondrial disorders comprise a heterogeneous group of diseases with multisystem involvement including myocardium. Most cases of mitochondrial cardiomyopathy are associated with myopathy and encephalopathy and are generally present in infancy or childhood. The disease often exhibits a rapid downward course with death frequently occuring within the first year of life. We describe a unique case of hypertrophic cardiomyopathy due to mitochondrial DNA mutation m.3303C >T in the MT-TL1 gene, diagnosed accidentally in a 35-year-old male. The patient initially presented with stroke of assumed cardioembolic origin due to the presence of two interatrial communications associated with mobile aneurysm of the interatrial septum. No other extracardiac manifestations of mitochondrial disorder were observed.