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To identify the clinical profile and aura characteristics of patients with Migraine with Aura (MwA) having acute cerebral ischemia, we compared stroke phenotype and risk factors in stroke patients with (S+MwA+) or without (S+MwA−) MwA and aura features in MwA patients with (S+MwA+) or without (S−MwA+) stroke. In this retrospective multicenter case–control study, we reviewed stroke phenotypes and vascular risk factors in S+MwA+ and S+MwA− patients younger than 60 years and risk factors and aura type, duration, onset age, and the frequency in the previous year in S+MwA+ patients and S−MwA+ subjects matched for age and disease history, investigated for patent foramen ovale (PFO). 539 stroke (7.7% S+MwA+) and 94 S−MwA + patients were enrolled. S+MwA+ patients were younger (p =.0.004) and more frequently presented PFO [OR 4.89 (95% CI 2.12–11.27)], septal interatrial aneurism [OR 2.69 (95% CI 1.15–6.27)] and cryptogenic ischemic stroke (CIS) [OR 6.80 (95% CI 3.26–14.18)] than S+MwA− subjects. Significant atherosclerosis was not detected in S+MwA+ patients. Compared to S−MwA+, S+MwA+ patients were characterized by visual [OR 3.82 (95% CI 1.36–10.66)] and shorter-lasting (20.0 min IQr 13.1 vs 30.0 min IQr 25.0; p