Abstract An antenatally diagnosed hypoplastic left heart syndrome boy from Kuwait was transferred in utero for postnatal surgical management. He was born to a nonconsanguineously married couple by spontaneous delivery at 33 + 5 weeks of gestation with a birth weight of 2.4 kg. He was on prostaglandin infusion after birth and shortly underwent bilateral pulmonary artery banding with gore-tex shunts (aorta to pulmonary artery shunts) to let him grow and get over his prematurity for his cardiac surgical palliative procedures. He had some right upper lobe collapse, which was treated with physiotherapy and suctioning to proceed for his first stage cardiac surgical repair (Norwood I). Following this, he had a rough course owing to his cardiac condition but was extubated without many problems in due course. He was persistently tachypnoeic, had two episodes of acute decompensations during his stay due to his lung segment collapse needing invasive ventilation, and was very fragile, needing careful management. He needed noninvasive positive pressure ventilation at other times even when stable, to keep his airways from collapsing. He underwent a bronchoscopy and CT scan when stable enough to do it that showed a normal airway but with thick, tenacious, and clear secretions on bronchoscopy while a CT showed some areas of atelectasis and pulmonary interstitial emphysema. He was investigated for cystic fibrosis and primary ciliary dyskinesia as other causes that could lead to persistent and recurrent atelectasis were ruled out and his acute episodes dealt with appropriately. His genetic testing results have confirmed the clinical diagnosis of primary ciliary dyskinesia and he is being discussed for further management from a multidisciplinary point of view.