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Hypoxia can occur after repair of transposition of great arteries. The most common cause of right to left shunt after arterial switch surgery is related to increased right ventricular pressures and persistent neonatal pulmonary arterial hypertension. We report a case of TGA repair causing right to left shunt with normal right ventricular pressures. Persistence of Eustachian valve with patent foramen ovale (PFO) is the unusual cause of hypoxia and desaturation. The patient was successfully managed by excision of Eustachian valve and closure of PFO.