Atlanto-axial subluxation (AAS) presents with marked frequency among patients with instability in rheumatoid arthritis (RA) patients. This study investigated the morphology of the atlanto-occipital joint (AOJ) in AAS patients due to RA using computed tomography, and examined the relationship between its morphology and other radiographic results Twenty-six consecutive patients with AAS due to RA treated by surgery were reviewed. In all patients, the AOJ was morphologically evaluated using sagittal reconstruction view on computed tomography before surgery. Moreover, the ADI value was investigated at the neutral position, and atlanto-axial angle (AAA) at the neutral and maximal flexion position in preoperative lateral cradiographs. The morphology of the AOJ was classified into three types as follows: a normal type which showed a maintenance of the joint space, a narrow type which showed a disappearance of the joint space and a fused type which showed the fusion of the AOJ. The pre-operative CT image of the AOJ demonstrated a normal type bilaterally in six cases (Group A). In 15 cases (Group B), CT image demonstrated narrowing on at least one side of the AOJ. In five cases (Group C), CT images demonstrated fusion on at least one side of the AOJ. The average ADI value at the flexion position was 10.7 mm in Group A, 11.7 mm in Group B, and 12.6 mm in Group C. There was no significant difference among those groups. The average ADI value at the neutral position before surgery was 2.8 mm in Group A, 5.9 mm in Group B, and 10.4 mm in Group C. There was no significant difference between Group A and B, and Group B and C; however, there was a significant difference between Group A and C (p < 0.004). The average AAA value was 25.3 degrees in Group A, 19.3 degrees in Group B and 3.4 degrees in Group C. There was no significant difference between Group A and B; however, there was a significant difference between Group A and C (p < 0.002), and Group B and C (p < 0.007). This study showed that fusion or ankylosis of the AOJ induced an enlargement of the ADI and anterior inclination of the atlas in the neutral position—despite the fact that normal findings of AOJ showed a slight displacement of the atlas to axis in RA patients showing AAS involvement.