IntroductionTracheal agenesis is a very rare congenital airway anomaly. It may pose a great challenge to the first attending physician both in diagnosis and in establishing the airway during the first day of life.Case presentationWe report a newborn Malay baby boy with trachea agenesis (type III by Floyd's classification) who presented with severe respiratory distress immediately after birth. Clinical diagnosis in this case was not straightforward, as it started with difficulty in intubation followed by an unsuccessful emergency tracheostomy in the neonatal intensive care unit. Urgent surgical neck exploration with endoscopic examination in the general operating theatre revealed the final diagnosis. The authors present a short description of the embryopathology and diagnostic criteria of the abnormality.ConclusionWe hope this case presentation will be valuable in increasing the awareness of physicians about this rare cause of tracheal obstruction or difficult intubation.