Migraine is associated with stroke-like episodes in mitochondrial encephalomyopathy, lactic acidosis, stroke-like syndrome (MELAS). Moreover, abnormalities of oxidative phosphorylation are also reported in migraine. We studied two maternal lineages with MELAS and chronic progressive external ophthalmoplegia (CPEO) affected probands carrying the 3243 A>G tRNA^Leu (MELAS) mutation, remarkable for a high frequency of subjects suffering only migraine. Thus, migraine could be a monosymptomatic expression of the MELAS mutation. We assessed the 3243 A>G tRNA^Leu mutational load in skeletal muscle and other somatic tissues from the migraine-only subjects, as well as lactic acid levels after exercise. All migraine-only subjects did not carry the MELAS mutation. Muscle biopsy showed mild mitochondrial abnormalities in the non-mutant, migraine-only subjects and, occasionally, abnormal lactic acid. Clear features of mitochondrial myopathy and pathological lactic acid characterised the subjects carrying the MELAS mutation. Our study demonstrates that migraine-only subjects lacked the MELAS mutation, but still had a possible mtDNA-associated genetic predisposition, being maternally related and having some evidence of impaired mitochondrial oxidative phosphorylation.