An 18-year-old asymptomatic female who was candidate for vaginal reconstruction surgery due to Mayer–Rokitansky–Küster–Hauser (MRKH) syndrome was referred to our tertiary care center following incidental finding of right sided cardiac chamber enlargement and severe pulmonary arterial hypertension in a transthoracic echocardiography performed prior to the gynecologic surgery. The patient had uterine agenesis and primary amenorrhea with normal external genitalia. She showed normal developmental and pubertal milestones. On genetic study she had normal female karyotype of 46, XX. In physical examination there was scoliosis of the spinal bones. Chest X-ray depicted dilated pulmonary artery, right ventricular enlargement and scoliosis. In twelve lead ECG there was normal sinus rhythm and right axis deviation. Transthoracic echocardiography showed right ventricular dilation and estimated systolic pulmonary artery pressure of about 93 mmHg. Transesophageal echocardiography was performed and showed no intra-cardiac shunt. There was also no bubble passage during contrast injection with and without provocative maneuvers. Laboratory data were negative for autoimmune and rheumatic causes of pulmonary hypertension. We found a relatively low platelet count of 118,000 per microliter of blood plus mild increases in liver enzymes and total bilirubin levels. Although the patient had previously undergone abdomino-pelvic sonography for her gynecologic problems that only reported uterine agenesis, we decided to perform a repeat sonography in search for possible liver abnormalities or portal hypertension with regards to unexplained thrombocytopenia. Interestingly abdominal sonography showed that the portal vein was totally absent and right liver lobe was atrophic. Further evaluation by abdominal CT-angiography revealed congenital absence of intra-hepatic portal branches with direct drainage of abdominal veins to inferior vena cava resulting in extra hepatic porto-systemic shunt in favor of Abernathy type 1 visceral malformation. There was also gut malrotation and evidence of MRKH syndrome with underdeveloped uterus and normal ovaries. Computed tomographic angiography of the heart and pulmonary arteries showed no evidence of pulmonary parenchymal involvement and no chronic pulmonary thromboembolic disease or vascular shunts. Right heart catheterization data confirmed severe pre-capillary pulmonary hypertension with pulmonary arterial pressure of 100/40 mmHg, normal cardiac output, normal capillary wedge pressure and no left to right shunts. Abdominal vascular angiography showed the complete absence of portal vein with splenic and superior mesenteric veins confluence draining directly to inferior vena cava forming a mesentero-systemic shunt. Unfortunately as the portal vein was entirely absent elimination of the porto-systemic shunt by interventional or surgical methods was not possible. The patient is a candidate for future lung and liver transplantation and was discharged home on pulmonary vasodilator therapy with sildenafil and macitentan.