Purpose To ascertain the anatomic and radiological parameters of the atlas (C1) pedicle and to explore a preferable method of C1 pedicle screw insertion. Methods Thirty-four conserved human cadaveric cervical spines (20 males, 14 females) underwent computed tomography (CT) scanning. Trajectories P (perpendicular to the coronal plane) and I (with medial inclination) were designed for each C1 pedicle on CT images. External pedicle wall width, medullary cavity width, transverse angle, and optimal entry point along each trajectory were measured. Cortical screws of 3.5 mm in diameter were inserted into C1 pedicles along trajectory P and I, respectively, and wall perforation was assessed (post-operative CT scanning). Results The external pedicle wall width and medullary cavity width along trajectory I were significantly wider than trajectory P (P<0.01). Although external pedicle wall widths were all greater than 3.5 mm, medullary cavity width<3.5 mm was found in 16.1 % pedicles along trajectory P and only 2.9 % along trajectory I. Transverse angle was 21.8°along trajectory I and 0°along trajectory P. Optimal entry point of trajectory I was 4.1 mm lateral from that of trajectory P. The lateral wall perforation rate was significantly lower along trajectory I than trajectory P (P<0.05). Conclusions C1 pedicle screw trajectory with medial inclination and more lateral entry points yielded wider medullary cavity width than that perpendicular to the coronal plane, and might minimize lateral wall perforation.