Abstract The ultrastructure and the permeability to macromolecules of the endothelia in the branched and unbranched regions of the arteries were compared using two different age groups (3 and 12 months) of rats. In the aortic arch, the endothelial cells were longer and thinner and contained fewer intracytoplasmic vesicles than those observed in the unbranched regions of aorta. Quantitative study revealed that the volume density of intracytoplasmic vesicles in the branched regions of aortic arch in 3-month-old rats was significantly ( P < 0.01) lower than the density value in the unbranched regions of aorta. The volume densities of vesicles in both regions of the aorta were lower than those in the carotid artery. There was an apparent increase in the frequency of the simple type of interendothelial contacts and a decrease in the complex type in the branched regions as compared with those in the unbranched regions of aorta and carotid artery. In addition to the normal interendothelial contacts, several open junctions with increasing width (25–300 nm) were identified in the branched regions of aortic arch and the bifurcations of carotid artery. For rats at the age of 12 months, local areas of the subendothelial space were expanded. Basal lamina-like and electron-dense materials were accumulated in the subendothelium. The volume densities of vesicles in the aortic endothelia were significantly ( P < 0.01) increased as compared with those in the 3-month-old group. The volume density of vesicles in the aortic arch was again significantly ( P < 0.01) lower than that in the unbranched regions of aorta. Furthermore, the frequency of the simple type of intercellular contacts was increased, whereas that of the complex type was decreased in both regions of aorta. With regard to the junctional complexes, the frequencies of gap junctions and tight junctions were increased and the junctionless intercellular contacts were decreased compared with those of the 3-month-old group.