Intimal thickening may be focal in nature and is especially found in areas with low shear rate. To be able to study the relation between intima-media thickness (IMT) and wall shear rate appropriately, a method to assess IMT locally is required. It was the aim of the present study to investigate the ability of a recently developed automated method to assess local differences in IMT, if any, in relatively short arterial segments. Therefore, intrasession interlocation differences in IMT were assessed at the posterior wall of the common carotid artery close to the bulb (0 mm) and 10 and 20 mm more upstream in terms of mean difference ± 2 standard deviations. Prior to this study we investigated the ability of the system to reproducibly assess IMT locally (intersession intralocation) in terms of repeatability coefficient (= 2 standard deviations). The measurements were performed in the common carotid artery 20 mm proximal to the bulb. The study was performed on young and older subjects presumed to be healthy. The intersession intralocation repeatability coefficient was 0.07 mm in the young group and 0.11 mm in the older group. The IMT close to the bulb (0 mm) was significantly larger (±0.050–0.065 mm) than that at the other locations in both age groups. We conclude that local IMT can be assessed reproducibly and local differences in wall morphology in short arterial segments can be studied reliably.