The permeability of exchange microvessels is regulated through complex interactions between signaling molecules and structural proteins in the endothelium. Endothelial barrier integrity is maintained by adhesive interactions occurring at the cell-cell and cell-matrix contacts via junctional proteins and focal adhesion complexes that are anchored to the cytoskeleton. Cyclic AMP (cAMP) and cAMP-dependent kinase counteract with the nitric oxide (NO)-cyclic GMP (cGMP) pathway to protect the basal barrier function. Upon stimulation by physical stress, growth factors, or inflammatory agents, endothelial cells undergo a series of intracellular signaling reactions involving activation of protein kinase C (PKC), protein kinase G (PKG), mitogen-activated protein kinases (MAPK), and/or protein tyrosine kinases. The phosphorylation cascades trigger biochemical and conformational changes in the barrier structure and ultimately lead to an opening of the paracellular pathway. In particular, myosin light chain kinase (MLCK) activation and subsequent myosin light chain (MLC) phosphorylation in endothelial cells directly result in cell contraction and shape changes. The phosphorylation of beta-catenin may cause disorganization of adherens junctions or dissociation of vascular endothelial (VE)-cadherin-catenin complex from its cytoskeletal anchor, leading to loose or opened intercellular junctions. Additionally, focal adhesion kinase (FAK) phosphorylation-coupled focal adhesion assembly and redistribution provide an anchorage support for the conformational changes occurring in the cells and at the cell junctions. The Src family tyrosine kinases may serve as common signals that coordinate these molecular events to facilitate the paracellular transport of macromolecules. The critical roles of protein kinases in endothelial hyperpermeability implicate the therapeutic significance of protein kinase inhibitors in the prevention and treatment of diseases and injuries that are associated with microvascular barrier dysfunction.