Congenital heart disease represents a condition commonly associated with pulmonary arterial hypertension (PAH). Eisenmenger syndrome is on the extreme end of the spectrum of PAH in the setting of congenital heart disease. This status implied the irreversibility and inoperability of a subgroup of patients with congenital heart defects. Untreated or even treated, Eisenmenger syndrome is characterized by a progressive increase in pulmonary vascular resistance that leads to right ventricular failure and death. Today, although there have been many advances in understanding of the pathophysiology of Eisenmenger syndrome and also advances in treating this disease, there is still no cure for this progressive condition, but the new vasodilators may be well tolerated and they improve the exercise capacity and hemodynamics without compromising the peripheral oxygen saturation. Eisenmenger syndrome can be prevented in most pediatric patients. With the advances in imaging, surgery and intensive care facilities and also in the early definitive therapy for the majority of lesions associated with a risk of developing Eisenmenger syndrome, a progressive decrease in the prevalence of this disease may be expected. Identifying the risk factors is problematic as the annual mortality rates are relatively low for Eisenmenger patients. We review here the available data on the pathophysiology, clinical presentation, prognosis and management of pulmonary arterial hypertension in patients with congenital heart disease.