Abstract Background Thyroglossal duct remnants, most frequently presenting as cysts, are the most common congenital anomalies of the neck. Bronchogenic cysts are rare congenital anomalies of the primitive foregut and are a subtype of foregut supplication cysts. Those cysts are the most common cystic lesions of the mediastinum. They can present in other areas such as the neck. Such cystic lesions are usually seen in pediatric population and symptomology depends on the location, size and degree of compression to the surrounding structures. The synchronous presence of both lesions in one patient is rare. To the best of our knowledge, such presentation has not been reported in the literature. We present a case of multiple lesions in the neck and mediastinum including precricoid, paraglotttic and paratracheal regions. Case Presentation A full-term male newborn presented in day 1 post normal vaginal delivery with progressive stridor and decreased feeding. Urgent airway endoscopy revealed a left supraglottic cyst and proximal non pulsatile tracheal wall compression by another cystic lesion. Aspiration of the supraglottic cyst was done and one month later, he developed stridor again for which he had endoscopic marsupialization of right supraglottic cyst and internal aspiration of paratracheal cyst. MRI showed right paratracheal cystic lesion with evidence of a tubular tract and an infected cyst inferiorly. Decision was made to explore the neck for definite removal of the cysts. Three lesions were identified: a precricoid mass, and paraglottic and paratracheal cysts. Cervical lesions were carefully dissected and excised. For the paratracheal cyst which extended to the mediastinum, incision and drainage was done and part of cyst wall was excised, and a drain inserted into the cyst. Histopathology confirmed the precrcoid lesion to be a thyroglossal duct remnant, the paraglottic cyst in keeping with bronchogenic cyst and the paratracheal cyst wall showed granulation tissue. Discussion The fact that the embryological basis for development of thyroglossal duct cyst and bronchogenic cyst is different makes diagnosis of both lesions is challenging and such presentation is unique. Definite diagnosis depends on accurate history, imaging particularly MRI and histopathology. Surgery is the treatment of choice for symptomatic cases.