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Holt-Oram syndrome comprises a rare spectrum of congenital cardiovascular and appendicular skeletal anomalies. However, only a few cases have reported lung involvement in Holt-Oram syndrome. We reported the rare case of a 1-year-old male child patient who presented with upper limb abnormalities and respiratory distress and was diagnosed with pulmonary agenesis and pulmonary arterial hypertension secondary to an atrial septal defect.