As some researchers theorized that cervicogenic headache (CEH) might be related to bony and discal features of the cervical spine, this retrospective study examined the shapes of the cervical vertebrae and intervertebral discs (IVDs) of individuals with CEH and compared them to asymptomatic controls. Scans of 40 subjects in their late 20’s–mid 30’s affected with CEH and 40 asymptomatic controls were obtained (overall = 19,040 measurements, age-sex matched, 20 males and 20 females in each group). The following cervical spine variables were measured: Supine lordosis, vertebral body-heights, A-P lengths, mediolateral widths and sagittal-wedging; IVDs heights and sagittal-wedging; pedicle heights, widths and transverse angles; laminar widths and transverse angles; articular facet angles, spinal canal, and transverse foramen lengths, widths, and areas. Both groups had similar shape variation along the cervical in all the measured parameters. There were no significant left–right differences in all measured parameters and no significant differences between the CEH and control groups concerning sex and age. Cervical IVDs were lordotic in shape, whereas their adjacent vertebral bodies were kyphotic in shape except for C2. In conclusion, the shape of the cervical spine and IVDs in subjects in their late 20’s–mid 30’s affected with CEH is identical to asymptomatic controls.