In this article, we present results of the study of blebbing activity of membranes of peripheral blood lymphocytes, concentrations of soluble platelet/endothelial cell adhesion molecule 1, and vascular endothelial growth factor (VEGF) in patients with pulmonary arterial hypertension associated with congenital heart diseases. The research has shown that hypoxia and hemodynamic factors are the initiators of blebbing of membrane of peripheral blood lymphocytes. The activity of blebbing increases in parallel with the severity of the disease. Aberrant leukocyte-endothelial interactions lead to the breach of athrombogenic endothelium function, hypercoagulation and risk of thrombosis. Revealed overexpression of VEGF, aimed at restoration of endothelial cells, has been most pronounced in cyanotic congenital heart defects. We suggest that the potentiating effect of apoptosis and endothelial cells' proliferation is a key factor of irreversibility of pulmonary arterial hypertension in congenital heart defects.