Cervical atlas alignment changes are associated with craniofacial development. Disturbance of craniofacial development may be associated with temporal mandibular joint function. Therefore, we examined the possibility of a correlation between unilateral missing teeth and morphologic changes of the spine and posture. We collected eighty-nine patients (38 men and 51 women) with unilateral posterior missing teeth and twenty patients without previous orthodontic treatment or missing posterior teeth by tracing and analyzing their panoramic and cephalometric film. We measured the angulations of articular eminence, cranio-cervical angle, and the percentage of the occlusal plane passing through the first and second cervical vertebrae with other morphologic geometric data. The angle of articular eminence inclination was higher in the non-missing teeth group than the missing teeth group (46.66° and 42.28°, respectively). The cranio-cervical angle was smaller in the missing posterior teeth group than the non-missing posterior teeth group (99.81° and 103.27°, respectively). The missing teeth group also showed fewer occlusal planes passing through the intersection of the first and second cervical vertebrae compared to the non-missing teeth group (28.9% and 65%, respectively). Individuals with unilateral missing teeth had lower articular eminence inclination, smaller cranio-cervical angle, and a lower percentage of the occlusal plane passing through the intersection of the first and second cervical vertebrae.