Hypoxia is a common cause of persistent pulmonary hypertension in the newborn (PPHN), a condition associated with endothelial dysfunction and abnormal pulmonary vascular remodeling. The GTPase RhoA has been implicated in the pathogenesis of PPHN, but its contribution to endothelial remodeling and function is not known. We studied pulmonary artery endothelial cells (PAECs) taken from piglets with chronic hypoxia-induced pulmonary hypertension and from healthy animals and analyzed the roles of Rho GTPases in the regulation of the endothelial phenotype and function under basal normoxic conditions, acute hypoxia, and reoxygenation. The activities of RhoA, Rac1, and Cdc42 were correlated with changes in the endothelial cytoskeleton, adherens junctions, permeability, ROS production, VEGF levels, and activities of transcription factors hypoxia-inducible factor (HIF)-1alpha and NF-kappaB. Adenoviral gene transfer was used to express dominant-negative GTPases, kinase-dead p21-activated kinase (PAK)-1, and constitutively activated Rac1 in cells. PAECs from pulmonary hypertensive piglets had a stable abnormal phenotype with a sustained reduction in Rac1 activity and an increase in RhoA activity, which correlated with an increase in actin stress fiber formation, increased permeability, and a decrease in VEGF and ROS production. Cells from pulmonary hypertensive animals were still able to respond to acute hypoxia. They also showed high activities of HIF-1alpha and NF-kappaB, likely to result from changes in the activities of Rho GTPases. Activation of Rac1 and its effector PAK-1 as well as inhibition of RhoA restored the abnormal phenotype and permeability of hypertensive PAECs to normal.