The clivus is a part of the sphenoid bone. It may show some anatomical variations such as fossa navicularis magna (FNM), canalis basilaris medianus (CBM) and craniopharyngeal canal (CPC). These variations have been associated with conditions like meningitis and tumors of skull base. Inadequate information about these structures may pose a risk of inaccurate diagnosis resulting in unwarranted interventional procedures. Hence, the knowledge about the prevalence of these variations is important. Thus, the objective of this study was to determine the prevalence of fossa navicularis magna, craniopharyngeal canal and canalis basilaris medianus and its types utilizing cone-beam computed tomography (CBCT) images.Retrospectively, a total of 350 CBCT scans were evaluated for the presence of FNM, CBM, its types and CPC. The analysis was done by two observers independently. Cohen's kappa statistics was used to determine the interobserver agreement.FNM was noted in 19.4% cases, CBM in 9.7% cases, whereas CPC was not identified in any case. Type 5 was the most common type of CBM. There was no significant difference (p > 0.05) between genders and age groups for the prevalence and a highly significant (p < 0.01) substantial agreement between observers for the prevalence of FNM and highly significant (p < 0.01) moderate agreement for the prevalence of CBM and its types was obtained.FNM, CBM, CPC, albeit rare anatomical variations of clivus, knowledge of these structures is important for radiologists, anatomists and surgeons to avoid misdiagnosis and provide awareness to the individual of a higher possibility of meningitis or tumors of the skull base.