We present a 31-year-old female who was admitted to our neurology department for vertigo, partial left-sided hemihypesthesia and nuchal headache of subacute onset. Colour-duplex ultrasound disclosed bilateral low flow with a high resistance flow pattern in both vertebral arteries in the V2 segments, while the basilar artery had normal flow. CT angiography and MRI ruled out any ischaemic cerebral infarct and disclosed a persistent hypoglossal artery (PHA) originating from the left internal carotid artery (ICA). The patient was eventually treated for cervicobrachialgia. Persistent carotid-basilar anastomosis such as PHA may account for an atypical stroke pattern in carotid disease, aneurysms and arterovenous malformations. In retrospect, PHA is amendable to colour-Duplex investigation due to an abnormal ICA flow and a discrepancy between the vertebral and basilar flow patterns. Ultrasound investigation of the vertebrobasilar system remains a challenge as variants appear frequently; hypoplasia of the vertebral arteries should thus be confirmed using CT or MR angiography.