PURPOSE: In this clinical investigation, we aimed (1) to re-evaluate the nature of glioneuronal tissue with transsphenoidal extension and how it fits into the nomenclature of midline malformations and mass lesions; (2) to find out if our imaging findings support current pathoanatomic concepts of clefts and canals in the sphenoid body of newborns. METHODS: In two neonates with respiratory distress due to nasopharyngeal masses, 3T MRI was performed, and CT in one of them. Imaging features were analyzed in consensus by two pediatric neuroradiologists with histological reports being available. An interdisciplinary panel compared the findings to those of case publications and differential entities from our institutional case collection. RESULTS: Referring to our rare case of transsphenoidal cerebral heterotopia and unique case of hypothalamic hamartoma with transsphenoidal herniation, glioneuronal heterotopia may definitely extend through the sphenoid bone. Consequently, there is reason for brain heterotopias to be labeled as such also in case of an intracranial component. Connection between heterotopic glioneuronal tissue in the nasopharynx and a hypothalamic hamartoma may go along with indistinct margins to normal brain. Neither extension through a transsphenoidal cleft nor association with a cleft palate are specific for cerebral heterotopia. Our findings support the hypothesis that transsphenoidal cerebral heterotopias do not or at least not invariably follow the route of Rathke's pouch, known as the craniopharyngeal canal. CONCLUSION: Transsphenoidal glioneuronal heterotopia should be the top differential diagnosis in MR imaging if a non-enhancing nasopharyngeal mass of an infant extends through a craniopharyngeal cleft within the intersphenoid synchondrosis.