To investigate the incidence and risk factors for adjacent segment degeneration (ASD) following occipitoaxial fusion (OAF) for atlantoaxial instability (AAI) in non-rheumatoid arthritis (RA). The study group comprised 41 patients without RA who underwent OAF due to AAI. Fifteen patients with postoperative ASD after OAF were classified as the ASD group, and the other 26 patients without postoperative ASD were included in the non-ASD group. There were 12 men and 3 women with a mean age of 43.52 years in the ASD group, and 19 men and 7 women with a mean age of 45.31 years in the non-ASD group. The mean follow-up period was 6.1 and 5.9 years in the ASD group and non-ASD group, respectively. Clinical outcomes and plain radiographs were retrospectively reviewed and compared between the two groups. The difference between pre- and postoperative O-C2 angles in the non-ASD group was significantly greater than that in the ASD group. The C2-7 angles changed significantly between the pre- and postoperative periods. It was suggested that the small O-C2 angle and large C2-7 angle observed in the early postoperative period were risk factors for the development of ASD. We also demonstrated a high incidence of subaxial subluxation (SAS) and swan neck deformity in the ASD group (27 versus 3.8% and 20 versus 0%, respectively). Under-correction of the O-C2 angle is likely to cause malalignment of the cervical spine, resulting in the development of postoperative ASD, SAS, and swan neck deformity.