Arteries for bypass grafting are harvested either with neighboring tissue attached or as skeletonized vessels that are free of surrounding tissue. There are significant benefits to skeletonization, but reports suggest that skeletonized vessels may develop structural defects and are at risk for atherosclerosis. We investigated the specific short‐term effects of skeletonization on carotid artery biomechanics and microanatomy in a rabbit model. Six carotid arteries were surgically skeletonized. To support healing, three of these received polyethylene glycol hydrogel injected along their exterior surfaces. M‐mode ultrasonography was used to track circumferential cyclic strain in the skeletonized, hydrogel‐treated, and contralateral vessels. On day 21, the arteries were harvested, and vessel structure was assessed by histology, immunofluorescence microscopy, two‐photon elastin autofluorescence, and second harmonic generation (SHG) microscopy. Intimal‐medial thickness appeared unaffected by skeletonization, but the SHG signals indicated significant changes in collagen turnover in the adventitia. Skeletonized arteries also exhibited significantly decreased radial compliance (circumferential cyclic strain dropped ∼30%) and decreased numbers of elastic laminae (9.1 ± 2.0 to 2.3 ± 1.4). Hydrogel treatment protected against these effects with treated vessels maintaining normal mechanical properties. These results indicate that arterial skeletonization triggers immediate effects on vessel remodeling and reduced vessel compliance resulting in specific tissue alterations within 21 days, but that these effects can be attenuated by the placement of hydrogel on the exterior surface of the skeletonized vessel.