The fossa navicularis is a relatively rare anatomic variation of the skull base. Awareness of its existence will avoid misinterpretations of radiological images and unnecessary investigations. This study describes the appearance of the fossa navicularis, and investigates its incidence and whether it is related to pathology at the basiocciput. We studied 492 dry human skulls and 525 computer tomography (CT) images of patients. Dry skulls showing a fossa navicularis were investigated by CT scan, whereas patients identified as having a fossa navicularis were further examined with magnetic resonance imaging (MRI). To document the position of the fossa more precisely, measurements were made between the fossa navicularis and certain anatomic landmarks such as the foramen ovale, the pharyngeal tubercle, the posterior border of the vomer, the foramen lacerum, the carotid canal, and the occipital condyle. Upon examination, 26 of 492 skulls (5.3%) were found to have a fossa navicularis. Twelve were <2 mm in depth and the other 14 had a depth of >/=2 mm. Of the 525 patients, 16 (3.0%) were identified as having a fossa navicularis in CT images. Evaluation of MRIs showed no soft tissue lesions in any of these patients. Comprehensive anatomic details of the fossa navicularis have not been reported in the literature. The results of this study may be useful to radiologists, anatomists, and surgeons interested in the skull base.