Cerebral aneurysms and arteropathies causing severe cerebrovascular events have been reported as rare complications in patients with late-onset Pompe disease. We investigated the frequency of cerebrovascular anomalies in six patients with late-onset Pompe disease followed at our institution. Clinical data collection and magnetic resonance angiography were performed as part of routine annual examinations. Four out of six patients had brain vascular anomalies including dolichoectasia of the basilar artery and ectasia of internal carotids. These patients also complained of gastrointestinal symptoms (chronic constipation and gastrointestinal reflux). Two patients had clinical signs related to the arteriopathy, including partial paralysis of the third cranial nerve and transient ischemic attacks. At 1 year follow-up, enzyme replacement therapy did not modify the size of cerebral vessels, but patients reported a marked improvement of intestinal symptoms. In conclusion, neurologists should be aware that intracranial artery abnormalities are not infrequent in patients with late-onset Pompe disease, and they should be specifically investigated in the presence of unexplained CNS symptoms.