In this double-blind, controlled, cross-sectional study, we compared structural changes in the cervical vertebrae of patients with nonradiographic axial spondyloarthropathy (nr-axSpA), patients with ankylosing spondylitis (AS), and a control group. We used the modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS) to determine whether the involvement of the cervical spine occurs earlier and is more severe than that of the lumbar spine in axial spondyloarthropathy (axSpA). A statistically significant difference was found in the total mSASSS between the AS and nr-axSpA groups (p = 0.038), but not in the cervical and lumbar mSASSS. Although the duration of the symptoms was shorter in the nr-axSpA group than in the AS group, no statistically significant difference was found in the cervical mSASSS between the AS and nr-axSpA groups. In both the AS and nr-axSpA groups, the cervical mSASSS values were found to be higher than the lumbar mSASSS values for the majority of the patients (82.8 and 89.5%, respectively). This may indicate that structural changes in the cervical spine occur during an early period of axSpA.