Objectives: The present study was undertaken to elucidate the role of Ala-9Val polymorphism of mitochondrial targeting sequence (MTS) of manganese superoxide dismutase (Mn-SOD, SOD2) in the pathophysiology of migraine. Methods: The polymorphism analyses were made in the blood of 73 patients with migraine and 90 healthy controls. Alanine or valine polymorphism in the MTS of SOD2 gene was evaluated using a primer pair to amplify a 107-bp fragment followed by digestion with restriction endonuclease NgoM IV. Results: No significant difference in genotype frequencies was found between migraineurs and controls. Subgroup analyses according to the clinical features of the patients according to their gender failed to identify any association between Ala-9Val polymorphism and the disease. Conclusions: The findings of the present study suggest that the polymorphism in MTS of SOD2 is not the cause of oxidative stress observed in migraine patients. Also, present results suggest no major modifying role for SOD2 polymorphism in migraine.