Migraine is a common neurological disorder characterized by debilitating head pain and an assortment of additional symptoms. Genes involved in neurological, vascular or hormonal pathways have all been implicated to play a role in predisposition towards developing migraine. All of these are nuclear encoded genes, but given the role of mitochondria in a number of neurological disorders and in energy production it is possible that mitochondrial variants may play a role in the pathogenesis of this disease. Few variants in the mitochondrial genome have so far been investigated in migraine. However one mitochondrial variant, an A to G substitution occurring at position 4336 of the mitochondrial genome has been associated with migraine in a previous study. We investigated two Australian Caucasian case-control populations and a Chi Square test indicated that there is a significant difference between case and control frequencies in one of our population cohorts, but given the lack of significance in the second cohort tested this may have been a sampling bias due to chance. We found the 4336 A>G variant to have a mildly protective effect in population one (p=0.0031) but no significance in the second population genotyped (p=0.3263). A second SNP, 4216T>C, was also investigated in both populations and was found not to be significantly associated with migraine in either cohort (p =0.3906 in population 1 and p=0.0714 in population 2). However we still hypothesise that development of migraine is influenced by mitochondrial dysfunction. The aim of this project is to conduct a complete mitochondrial genome scan to identify the full spectrum of mtDNA variation in a selection of migraine affected family samples and a number of samples from the genetic isolate Norfolk Island pedigree.