Patients presenting with thrombotic stroke of unexplained etiology and or migraine with aura were screened for mitochondrial (mt) DNA mutations associated with cytopathies given that both migraine and stroke-like episodes are recognised with certain mt DNA mutations. Mutations usually associated with either mitochondrial encephalopathy, lactic acidosis and stroke-like episode, myoclonic epilepsy with ragged red fibres, or those strongly linked to Leber's hereditary optic neuropathy (LHON) were not detected in patients or controls. However, increased levels of two of the secondary LHON mutations were found. The T-->C mutation at nucleotide 4216 was more common than expected in patients aged 35 years or less, as was the 13708 G-->A mutation in young stroke patients. This data lends support to the possibility that an accumulation of minor mt DNA mutations may contribute to the pathoaetiology of stroke and migraine with aura in some young patients.