We report the CT and MR characteristics of a newborn with a rare, complex malformation characterised by a large rhinopharyngeal and oropharyngeal enterogenous cyst, associated with an osseous defect of the basiocciput, called canalis basilaris medianus (CBM). A partial herniation of the bulb was demonstrated through the bony defect on the midline. The enterogenous cyst occupied the rhinopharynx and oropharynx, narrowing the pharyngeal lumen and making it difficult for the introduction of an orotracheal tube.