Background: Manifestations of typical migraine aura can be numerous. Investigation of its pathophysiological mechanisms can be challenging if a stratification of phenotypes is not performed. In this context, the Migraine Aura Complexity Score (MACS), recently developed, may help. Here we aimed to categorize migraine patients into homogenous groups using MACS and to compare those groups with respect to patients' characteristics and neuroimaging findings.Methods: Participants who have a migraine with aura (MwA) were interviewed after each attack in order to obtain the characteristics of migraine aura. Thereafter, we scored the complexity of their auras by MACS. The MACS was used to categorize patients into three groups: MwA-S (with simple aura), MwA-MC (with moderately complex aura), and MwA-C (with complex aura). The patient characteristics and estimated cortical thickness of regions of interest, which are potentially linked to the symptoms that develop during the aura, were used to compare these groups.Results: In total, 338 MwA attacks were recorded in analyzed groups. Scotoma was the most frequently reported symptom in the groups, followed by somatosensory aura in the MwA-C group and zig-zag lines in the MwA-MC and MwA-S groups. Patients in the MwA-C and MwA-MC groups had a thicker cortex in the left primary visual cortex with respect to MwA-S group. In addition, patients in the MwA-C group had a thicker cortex in several visual and somatosensory cortical regions relative to the MwA-S group.Conclusions: Our results show that the newly developed MACS can be used for the stratification of MwA patients, herewith allowing the better investigation of changes in migraineurs' brains.