This study was conducted to elucidate the comparative anatomical features of the skull of rabbits and cats using CT scans. Adult healthy New Zealand rabbits and Domestic Baladi cats of both sexes, were prepared for X-ray and CT scan of the heads at different positions. The heads were also processed for bone preparation and were photographed at various views. Some measurements were taken to exhibit the main differences between the two animal species. There was a cranial pharyngeal canal in the basisphenoid bone of rabbit, which was absent in cat. The retroarticular process situated caudal to the mandibular fossa in cat and absent in rabbit. The carotid foramen was large and situated only in rabbit ventromedial to the bulla tympanica. The supraorbital process of rabbit extended anteriorly and posteriorly forming rostral and caudal supraorbital fissures. The orbit was located laterally in rabbit rostrally in cat. The facial surface of the maxilla was perforated by several formina in rabbit. A large retroalveolar foramen was found only in the mandible of rabbit. The condyloid process of the mandible was large and present longitudinally in rabbit and transversally in cat. Also, the hyoid bones and the paranasal sinuses were compared at both animals. The hyoid bone located in the mandibular space in rabbit and caudal to this space in cat. The lingual process of the hyoid bone was absent in cat. The middle and great cornuae of the hyoid bone were absent in rabbit. The paranasal sinuses of rabbit were maxillary and ethmoidal sinuses. While in cat, there were frontal, sphenoidal and maxillary sinuses. The combination between the traditional gross morphology of the skulls, X-ray and scan aimed to clarify and confirm all the points of comparison between the two animal species used, which was not achieved by using only one method of them.