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Glial choristoma of the head and neck is a rare, benign congenital malformation consisting of a mass of heterotopic glial cells. In cases involving the upper aerodigestive tract, this can present with upper airway obstruction. In the acute setting, this can lead to diagnostic challenges due to the broad differential, as well as the additional difficulties in obtaining appropriate imaging and tissue samples due to the potential risk of airway compromise. We present a case of a neonate born with a large heterogenous mass involving the upper aerodigestive tract and multiple deep neck spaces which resulted in upper airway compromise requiring emergency surgical intervention in the form of a paediatric tracheostomy. We will discuss the histological findings which initially suggested a glial choristoma, work-up and treatment of this patient with the aim of supplementing the limited existing clinical knowledge of this congenital anomaly and understanding the implications of a paediatric tracheostomy in our setting.