Pulmonary hypertension is not the only cause of arterial desaturation in patients with atrial septal defect. Arterial desaturation can also occur with normal pulmonary artery pressure making it mandatory to understand the mechanism to avoid erroneous diagnosis. In this report, for the first time, we demonstrate atrial flutter as the cause of arterial desaturation in a patient with large atrial septal defect despite normal pulmonary artery pressure, which was normalised following successful radiofrequency ablation.