Migraine is associated with an increased risk of deep white matter lesions and subclinical posterior circulation infarcts. A significant association between deep white matter hyperintensities and cerebral atrophy is true for various neurological diseases; it was not specifically proven in migraine. The aim of this study was to evaluate the cerebellar and cerebral volume and volume ratios for cerebellum using the Cavalieri principle. We also aimed to examine whether migraine with aura causes cerebellar and cerebral atrophy. Twenty three right-handed patients with migraine with aura diagnosed by means of the International Headache Society criteria and 24 age-matched subjects whose only health problem was headache due to rhinosinusitis and tension type headache were included in the study. Measurements of the cerebellar and cerebral volumes as well as cerebellar/cerebral volume ratios were made using Cavalieri's principle by utilizing the point-counting methods. There were no significant differences between the volumes of cerebrum, cerebellum, and the ratio of cerebellum to cerebrum for males (p = 0.05, p = 0.10, and p = 0.64, respectively) and for females (p = 0.18, p = 0.89, and p = 0.24, respectively). Our results suggest that patients with migraine with aura do not have a significant difference in cerebellar and cerebral volumes and cerebellar/cerebral volume ratios compared to the non-migraine group.