Background. Congenital absence of the portal vein (CAPV) is an extremely rare malformation that is caused by aberrant venous development during embryogenesis and is usually associated with congenital portosystemic shunts (CPSS). This hemodynamic allows mesenteric blood to bypass the liver metabolism and causes an imbalance between vasodilators and vasoconstrictors in the pulmonary circulation, which, again, might lead to the development of secondary portopulmonary hypertension (PoPH). Establishing the exact morphology of the splanchnic venous system is important when evaluating possible therapeutic options (differentiating type I and II CAPV), because some variants enable the closure of the shunt, and this represents a potential cure for pulmonary arterial hypertension (PAH). Once PoPH is diagnosed, complex care in a specialized expert centre is necessary. If possible, CPSS closure is recommended. For long-term successful patient management, specific targeted PAH therapy administration is crucial. Significant morbidity and mortality in these patients may result not only from PAH itself but also due to specific PoPH complications, such as compression of the left main coronary artery by pulmonary artery aneurysm. Case Report. We report on two patients with PoPH due to CAPV and CPSS (without any liver disease) who presented as severe PAH and who, before admission to our expert centre, were misdiagnosed as idiopathic PAH. The case reports also represent our experience with respect to the long-term follow-up and PAH-specific medical treatment of these patients, as well as the possible (even fatal) complications of these rare and complex patients.