A mathematical model of diffusive transport of macromolecules across the arterial wall was developed in order to analyze the enhancement of molecular transport into the media in the presence of the endothelial injuries. The model is based on the continuum description of the distribution of macromolecules in the arterial wall with multiple injuries periodically dispersed on the endothelial surface. A boundary element method is successfully employed to model the problem geometry along with the relevant boundary conditions. The concentration and surface flux are computed for various physical conditions of the artery. Among other factors, the proper estimation of the mass transfer resistance, characterized by the Biot number, of the endothelial surface is crucial for the analysis. In addition the curvature effects are negligible when the vessel radius is larger than 10 times the wall thickness.