The remodeling process of the arterial wall in atherosclerosis involves intimal thickening, which can be related to the barrier functions of the endothelial cell layer (ECL) and internal elastic lamina (IEL). To evaluate the ECL and IEL permeabilities (P_ECL, P_IEL) and intimal transport parameters, viz., apparent HRP velocity (V_I) and diffusivity (D_I), we compared simulations with a mathematical model to experimental data. We injected HRP into apolipoprotein E (apoE)-null mice and measured HRP concentration profiles in lesioned areas of aortas. Lesion size was characterized by lower, middle, and upper ranges of the intimal/medial thickness: 0<_I/_M0.5, 0.5<_I/_M1.0, _I/_M>1.0. The P_ECL (µm/min) of 5-month old mice in the middle range (0.98±0.14) was significantly greater than that in the lower range (0.21±0.03), but not significantly different from mice in the upper range (0.99±0.55). The P_ECL of 12-month old mice increased significantly with the relative intimal thickness: 0.27±0.04 in the lower range, 1.12±0.15 in the middle range, and 1.74±0.24 in the upper range. In both age groups, V_I (µm/min) increased significantly from lower to upper ranges of intimal thickness. However, P_IEL did not change significantly with relative intimal thickness and age. In the upper range of intimal thickness, P_ECL and V_I were significantly greater in 12-month old mice than in 5-month old mice. These data indicate an interaction between lesion growth and aging that leads to progressive loss in the integrity of the endothelial barrier function. Furthermore, the IEL is not a significant barrier between the intima and tunica media in the atherosclerotic process.