Introduction:The deformed joints seen in congenital atlantoaxial dislocation (CAAD) are often associated with vascular anomalies. It is important to identify these vascular anomalies and address them appropriately without compromising the manipulation and fusion of C1–C2 joints. The small bones in pediatric age group pose an additional challenge.Materials and Methods:Data of fifty-six children with CAAD operated in the last 4 years was analyzed. A computed tomography angiogram was obtained preoperatively to assess for the course of the third segment of vertebral artery (VA). The anomalous VA was dissected and safeguarded during drilling and manipulation of the C1–C2 joints.Results:Of the 112 VAs, 5 were aplastic, 21 crossed the joint posteriorly. Only one patient with reducible atlantoaxial dislocation (AAD) had anomalous VA crossing the joint posteriorly, the remaining VA anomalies were seen with irreducible AAD. Anomalous VA was seen on both sides in 2 patients. The most common anomaly was an inverted VA seen in seven sides. In all patients, the anomalous VA could be dissected and safeguarded without compromising the C1–C2 dissection and manipulation and fusion. In children, even the normal VA may occasionally pose difficulties while manipulation of joints. Challenges while addressing the anomalous and normal VA in pediatric age group have been described. Techniques to overcome these have been discussed.Conclusion:It is important to delineate the anomalous VA. However, the presence of such an artery is not a deterrent to the manipulation of C1–C2 joint, essential for best results. Special attention needs to be paid to the extent of distraction, medial C2 transverse foramen, and dissection/drilling of the area superior to the anomalous VA in the pediatric age group.