Heparan sulfate (HS) is ubiquitous throughout the human body. The backbone of HS is composed of many types of sugars. HS serves as a docking site for a vast array of protein ligands. Recent evidence suggests a unique diversity in HS structure that alters protein binding and protein function. This diversity in HS structure has been overlooked till now. The goal of this study was to determine whether femoral artery wire injury modified HS structure. Femoral artery wire injury was performed in 16-week-old male C57BL6 mice. Transcript levels of a panel of enzymes that regulate HS fine structure, including N-deacetylase-N-sulfotransferases (Ndst) 1 and 2, exostoses (Ext) 1 and 2, C5 epimerase, and 2-O and 6-O sulfotransferases, were quantified with real-time quantitative polymerase chain reaction at 7 and 14 days post injury. All enzymes showed significant alterations in messenger RNA expression in response to injury. Ndst1, the most prevalent isoform, exhibited a 20-fold increase in response to injury. Injury induced significant alterations in fine structure specially increases in N-sulfated disaccharides at 14 days post injury. Vascular injury invokes transcriptional regulation of the enzymes that regulate HS structure, as well as changes in the pattern of HS chains in the vessel wall 14 days post injury. These findings may be important as the foundation of altered growth factor and chemokine binding in the process of vascular remodeling.