Introduction There are many craniometric measurements that are used in evaluating craniovertebral junction (CVJ) pathologies such as basilar invagination, atlantoaxial dislocation and platybasia. Therefore, it is important to determine the normal reference range of the craniometric measurements. This study aims to determine the morphometric reference values of the bony structures in the CVJ from cone-beam computed tomography (CBCT) images of a group of South Eastern Anatolian population. Materials and methods The CBCT images of 300 individuals were retrospectively evaluated. 14 parameters on midsagittal and 2 parameters on the coronal plane were studied. The data were statistically evaluated. Results Measurement results were found as follows; the distances between odontoid process (OP) and McGregor line as 0.31 +/- 3.22 mm, OP and Chamberlain line 1.06 +/- 3.22 mm, OP and McRae line 5.30 +/- 1.59 mm, OP and Fischgold digastric line 8.70 +/- 4.12 mm, OP and Fischgold bimastoid line - 5.15 +/- 4.86 mm, length of McRae line 35.58 +/- 2.52 mm, atlantodental interval 1.28 +/- 0.48 mm, posterior atlantodental interval 19.54 +/- 2.24 mm, basion axial interval 4.01 +/- 1.83 mm, basion dental interval 4.92 +/- 1.77 mm, length of Modified Ranawat line 28.66 +/- 2.38 mm, length of Redlund-Johnell line 35.11 +/- 4.09 mm, clivus canal angle 157.62 degrees +/- 11.85 degrees, Welcher basal angle 130.83 degrees +/- 6.29 degrees, craniocervical tilt 126.98 degrees +/- 12.24 degrees and Powers ratio as 0.72 +/- 0.06. Conclusion In this study, the morphometric values were evaluated according to age and gender in individuals who did not have any radiologic anomalies. The normal reference ranges may be useful for researchers who are researching pathology in this region. It is recommended to conduct further studies with different populations to determine the normal reference range.