The aim of this report is to present two cases of canalis basilaris medianus as identified on cone-beam computed tomography (CBCT) in the base of the skull. The CBCT data sets were sent for radiographic consultation. In both cases, multi-planar views revealed an osseous defect in the base of the skull in the clivus region, the sagittal view showed a unilateral, well-defined, non-corticated, track-like low-attenuation osseous defect in the clivus. The appearance of the defect was highly reminiscent of a fracture of the clivus. The borders of osseous defect were smooth, and no other radiographic signs suggestive of osteolytic destructive processes were noted. Based on the overall radiographic examination, a radiographic impression of canalis basilaris medianus was made. Canalis basilaris medianus is a rare anatomical variant and is generally observed on the clivus. Due to its potential association with meningitis, it should be recognized and reported to avoid potential complications.