Background The vertebral artery (VA) and atlantoaxial joint (AAJ), with complicated structures, are located in the depths of the head-neck boundary area, the regional anatomy of which cannot be shown globally and directly. This study aims to evaluate three-dimensional CT angiography (3DCTA) in displaying the AAJ, atlantoaxial segment of the vertebral artery (ASVA) and the identification of their interrelations.Methods Sixty-eight subjects without pathology of the ASVA and AAJ were selected from head-neck CTA examination. All the 3D images were formed with volume rendering (VR) together with techniques of separating, fusing, opacifying and false-coloring (SFOF). On the 3D images, the ASVA and AAJ were observed, and their interrelations were measured.Results All the 3DCTA images were of high quality and up to our requirements. They could cleady and directly show the ASVA, ascending along the AAJ. There were 5 curves in the course of the ASVA, of which 2 curves were away from the atlantoaxial joint, one in the 2nd curve of 0.0 mm-5.4 mm, the other in the 4th of 2.6 mm-9.2 mm. There was no significant difference in the measurements between left and dght (P>0.05). The curved parts of the ASVA slightly expanded, with the biggest diameter of 5.6 mm in the 4th curve. Statistical comparison shows that the left ASVA is larger than the right (P<0.05). Variations of the ASVA were found in 8 cases and of the AAJ in 12.Conclusions 3DCTA can globally and directly demonstrate the structures of the AAJ, ASVA and their interrelations. The 3D imaging data make up and enrich the research contents of regional anatomy and lay the foundation for related study and applications.