Subglottic cysts can cause stridor and respiratory distress in the infant. The diagnosis of subglottic cysts is often confirmed during direct laryngoscopy and bronchoscopy. We describe the case of a 6-month-old boy with bilateral subglottic cysts that were preoperatively diagnosed by magnetic resonance imaging (MRI). We also review the current literature on the diagnosis and treatment of subglottic cysts. Up until now, 63 cases of subglottic cysts were reported in the literature since 1966, and most were diagnosed by direct endoscopy. In this article, we describe a new case and we provide the first published report of the novel use of MRI in diagnosing this lesion.