Advances in the management of premature infants have resulted in improved survival. However, long-term intubation may produce associated laryngeal complications. We report 12 infants and children who developed subglottic cysts following long-term intubation as newborns. The majority of the cysts were in the posterior subglottic larynx. Laser excision of the cysts was undertaken in 8 patients and 3 underwent removal with cupped forceps. Recurrent cysts in 3 patients required more than one endoscopic procedure. The differential diagnosis of stridor in infants who have required long-term intubation includes subglottic cysts. The cysts are not always obvious at endoscopy and indeed may be buried below the mucosa within a soft tissue subglottic stenosis. Their presence may be suspected when tiny beads of mucus are released when laser surgery of a soft tissue stenosis is applied. Successful management of these cysts includes early precise diagnosis, with careful identification of these cysts to differentiate them from other types of subglottic stenosis. An initial attempt of conservative management with endoscopic excision is made. If this fails, an anterior cricoid split may be indicated in cases where the cysts are associated with soft tissue subglottic stenosis. Tracheostomy may be unavoidable in some cases.