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We present a case of sinus venosus atrial septal defect in a patient who was previously diagnosed as having primary pulmonary hypertension in a tertiary care center. Our findings are based on 2-dimensional trans-thoracic echocardiography, chest X–ray and surface electrocardiogram. A 26-year-old man, previously diagnosed as a case of primary pulmonary hypertension, presented to the emergency department (ED) with chest pain and breathlessness on exertion. Cardiac biomarkers were within their normal ranges. Surface electrocardiogram showed right atrial and ventricular overload with right axis deviation. Chest imaging noted enlarged central pulmonary vascularity with bilateral plethoric lung fields. Trans-thoracic echocardiography showed a dilated right atria and ventricle with severe tricuspid regurgitation and severe pulmonary artery hypertension with an intact atrial septum. Surprisingly, the transoesophageal echocardiogram revealed the presence of a sinus venous superior vena cava-type atrial septal defect with the right pulmonary vein draining into the right atria. In this full-text version, we present a more detailed discussion of sinus-venous atrial septal defect associated with partial anomalous pulmonary venous return that was wrongly diagnosed as a case of primary pulmonary hypertension in a tertiary care center.