It is known that the Circle of Willis (CoW) variations and white matter hyperintensities (WMHs) are common in migraine. This retrospective study aims to investigate the relationship between the CoW variations and WMHs in migraine without aura (MWoA) (n=38) and migraine with aura (MWA) (n=40) patients. Demographic, clinical and radiological findings (the CoW variations and WMH burden) of the patients were recorded, and the relationship between the variables was evaluated in both groups. The overall incomplete COW, incomplete anterior or vertebrobasilar portion of the CoW, or the presence of fetal PCA showed no significant difference between the MWoA and MWA groups (p > 0.05). An incomplete posterior portion of the CoW was significantly higher in the MWA group than in the MWoA group (p = 0.034). In the WMA group, the visual aura was present in 72% of patients with the overall incomplete CoW; all of these were posterior portion variations of the CoW. When the WMH burden was compared, no significant difference was seen between the MWoA and MWA groups (p > 0.05). Among patients with the CoW variations in the MWoA group, the rate of patients without WMHs was significantly higher (p = 0.030). No significant difference was observed between the CoW variations and WMH burden in the MWA group (p > 0.05). In conclusion incomplete posterior portion of the CoW is common in MWA, and this variation is associated with visual aura but unrelated to WMH burden.