Purpose The occipital condyles (OCs) are crucial anatomical structures in the cranial base. To our knowledge, there is no cone beam computed tomography (CBCT)-based study on the morphometric analysis of OCs. The aim of this study was to evaluate the morphometric analysis of OCs using CBCT. Methods CBCT images of 200 OCs from 100 patients of which 39 males and 61 females in the age group of 18-67 years were included in the study population. Linear and angular measurements of OCs were performed. Results The average OC width, length, height, sagittal angle, and effective height were 10.3 +/- 1.3 mm, 19.6 +/- 2.0 mm, 9.1 +/- 1.4 mm, 7.4 +/- 1.7 mm, and 35.3 +/- 5.2 mm. Condylar width and sagittal angle measurements were found significantly different between the right and left sides; and were not found significant difference between the right and left sides in the measurements of condylar height, length, and effective height. Also the average intercondylar anterior distance (ICAD), intercondylar posterior distance (ICPD), distance between the basion and the anterior apex of the occipital condyle (B-AAOC), distance between the basion and posterior apex of the occipital condyle (B-PAOC), distance between the opisthion and anterior apex of occipital condyle (O-AAOC), and distance between the opisthion and posterior apex of occipital condyle (O-PAOC) were 20.9 +/- 1.5 mm, 44.0 +/- 2.0 mm, 12.3 +/- 1.9 mm, 34.5 +/- 4.2 mm, 29.8 +/- 1.7 mm, and 27.0 +/- 2.1 mm. There was not significant difference in the morphometric measurements among age groups. All morphometric measurements showed a significant difference depending on gender. Conclusions The morphometric evaluation of OCs may be effectively examined using CBCT. Linear and angular measurements data of OCs in the present study may be used as a reference database for future morphometric and surgical investigations.