A 39-year-old man with a history of rupture of a sinus of Valsalva aneurysm experienced an ischemic stroke. Although the patient presented left-sided hemiparesis for a week, no abnormal signals were indicated on diffusion-weighted imaging with repeated magnetic resonance scans. Carotid ultrasound and cerebral angiography were conducted, and they revealed hypoplasty of the left internal carotid artery with a low-lying carotid bifurcation at the level of the C6 vertebra. In addition, he was diagnosed with intellectual disabilities, evaluated by the Wechsler Adult Intelligence Scale-III, and congenital velopharyngeal insufficiency. We herein present the first report of a patient with cardio-cerebrovascular abnormalities, intellectual disabilities, and an otorhinolaryngological abnormality.