Pulmonary hypertension associated with congenital systemic-to-pulmonary shunts has been classified, in the Evian-Venice classification, as Pulmonary Arterial Hypertension, which includes a heterogeneous group of conditions. Emerging options for treatment of patients with pulmonary arterial hypertension are related to those with the idiopathic form of the disease, but may also improve quality of life and survival in patients with pulmonary arterial hypertension associated with congenital cardiac disease. Despite the evident similarities in pulmonary vascular disease, it is important also to recognise the differences between patients in whom pulmonary arterial hypertension is the consequence of systemic-to-pulmonary shunts as opposed to those with other conditions. Patients with pulmonary hypertension associated with congenital cardiac disease themselves constitute a heterogeneous population, in which generalisation may be hazardous. Specific considerations need to be given to the type of cardiac diagnosis, the prognosis and evolution of pulmonary vascular disease, and the circulatory physiology before embarking on new strategies for medical treatment in the individual patient. In this review, we highlight the features that require specific attention in these patients. In addition, we discuss briefly the data currently available on the effectiveness of the new anti-proliferative drugs in patients with the Eisenmenger syndrome.