Atrial septal pouch (ASP) is a newly defined anomaly that results in interatrial septum fusion. The aim of the present study was to compare the incidence of ASP between patients with migraine and healthy volunteers. In addition, clinical characteristics of patients with migraine with aura were reviewed in order to reveal any correlation with cardiac imaging results. This study enrolled 26 patients suffering migraine with aura and 40 healthy volunteers. Age, sex, duration of headache, frequency and duration of attack, types of aura and pain, accompanying symptoms (such as nausea, vomiting, photophobia, and phonophobia), presence of dizziness, visual analog scale score, family history of migraine, history of risk factors for atherosclerosis, availability of drugs, neurological examination findings and cardiac imaging results were recorded. The odds ratio of having ASP in the presence of migraine with aura was 38.5% which is 30% in the healthy volunteers group (p<0.05). Compared with the group without atherosclerotic risk, the group with the risk demonstrated higher rates of ASP. Other clinical features demonstrated no significant differences (p>0.05). The results of the present study suggest that ASP is a prominent risk factor for distal embolization when observed in patients with migraine with aura. Cortical spreading depression is theorized to be related with microembolisms which originated from heart.