It has long been a research hotspot to diagnose atlanto-axial disorder by observing the shape and motions of atlanto-axial joints. The basis for correlative studies is to ascertain the normal anatomic features of atlanto-axial joints. In our study, 33 normal subjects were examined for atlanto-axial joints, by three-dimensional CT (3D-CT) in functional positions (neutral, left and right rotary position). The contraposition between superior and inferior articular facets of lateral atlanto-axial joints (AFLAJ), including its shape and type, the width of rotational facets displacement (RFD), head's rotational angle (HRA) and rotational angle at C(1-2) (RAC(1-2)) were observed and measured on 3D-CT images. In neutral position, a complete contraposition of AFLAJ was found in 25 subjects as well as a basic contraposition in 8. In rotary position, the width of RFD was between 6.16 and 8.68 mm, the angle of HRA was between 30.2 degrees and 45.8 degrees , and RAC(1-2) between 26.7 degrees and 38.9 degrees . There is no significant difference in RFD, HRA or RAC(1-2) (P > 0.05) in between levorotatory and dextrogyrate orientation, and there is a positive correlation between RFD and RAC(1-2) (r = 0.5078, P < 0.05). Our study results show that the contraposition of AFLAJ can be clearly displayed by 3D-CT, and complete or basic contraposition in neutral position and symmetry RFD, HRA and RAC(1-2) in rotary position, are the normal anatomic features of atlanto-axial joints.