Diagnostic imaging is one of the pillars in the clinical workup of horses with clinical signs of cervical spinal disease. An improved awareness of morphologic variations in equine cervical vertebrae would be helpful for interpreting findings. The aim of this anatomic study was to describe CT variations in left-right symmetry and morphology of the cervical and cervicothoracic vertebrae in a sample of horses. Postmortem CT examinations of the cervical spine for horses without congenital growth disorders were prospectively and retrospectively recruited. A total of 78 horses (27 foals, 51 mature horses) were evaluated. Twenty-six horses (33.3%) had homologous changes in which a transposition of the caudal part of the transverse process (caudal ventral tubercle) of C6 toward the ventral aspect of the transverse process of C7 was present (n = 10 bilateral, n = 12 unilateral left-sided, n = 4 unilateral right-sided). There was one horse with occipito-atlantal malformation, two horses with rudimentary first ribs bilaterally, and one horse with bilateral transverse processes at Th1, representing homeotic (transitional) vertebral changes. Chi-square tests identified no significant differences in the number of conformational variations between the group of mature horses with or without clinical signs (P = 0.81) or between the group of mature horses and the group of foals (P = 0.72). Findings indicated that, in this sample of horses, the most frequently identified variations were homologous variations (transposition of the caudal part of the transverse process of C6-C7) in the caudal equine cervical vertebral column. Homeotic (transitional) variations at the cervicothoracic vertebral column were less common.