Failure to detect dangerous anatomic vertebral artery anomalies (AVAAs) and dangerous functional vertebral artery anomalies (FVAAs) at the craniovertebral junction (CVJ) in patients with basilar invagination (BI) can result in major complications such as intraoperative vertebral artery injury, brain infarctions, and even death. Iatrogenic vertebral artery injury is a rare but severe complication of cervical spine surgery. We aimed to evaluate dangerous vertebral artery anomalies at the CVJ in patients with BI using computed tomographic angiography (CTA). CTA images of 61 BI patients were retrospectively analyzed to evaluate AVAAs and FVAAs at the CVJ. Dangerous AVAAs include a persistent first intersegmental artery (FIA), fenestration of the vertebral artery (FEN), and posterior inferior cerebellar artery with an extradural C1/2 origin (PICA-C1/2). Dangerous FVAAs include a dominant vertebral artery (DVA) and hypoplastic vertebral artery ending in the PICA (HVA-PICA) without joining the basilar artery. Overall, 31 female and 30 male patients (mean age, 42.3 years) were included. The incidences of FIA, FEN, and PICA-C1/2 were 29.5 % (18/61), 3.3 % (2/61), and 3.3 % (2/61), respectively, whereas the incidences of DVA and HVA-PICA were 36.1 % (22/61) and 1.65 % (1/61), respectively. Dangerous vertebral artery anomalies at the CVJ have a high incidence in patients with BI. Preoperative CTA is highly recommended in such patients to identify anomalous vertebral arteries and reduce the risk of intraoperative injury. Copyright © 2020 Elsevier B.V. All rights reserved.