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Migraine is a typically unilateral disorder in adulthood; however, the reasons for painful lateralization have been little investigated. The possible influence of manual dominance was suggested. We aimed to investigate the localization of pain in migraine attacks in right-handed and left-handed subjects. The retrospective study collected 546 patients with migraine aged between 16 and 65 years, reporting the manual dominance to the Edinburgh test. We included 466 right-handed and 80 left-handed subjects with migraine. We registered 4215 unilateral painful attacks. The right-handers had 3412 unilateral episodes; 62.8% of the attacks were characterized by pain on the right side and 37.2% by pain on the left. The left-handed subjects reported 803 unilateral pain with 63.5% of unilateral pain episodes on the left side and 36.5% of attacks with lateralized pain on the right (p < 0.001). Our data suggest that manual dominance may influence the side of pain lateralization in migraine.