The glycocalyx is a layer coating the luminal surface of vascular endothelial cells. It is vital for endothelial function as it participates in microvascular reactivity, endothelium interaction with blood constituents, and vascular permeability. Structural and functional damage to glycocalyx occurs in various disease states. A prominent clinical situation characterized by glycocalyx derangement is ischemia-reperfusion (I/R) of the whole body as well as during selective I/R to organs such as the kidney, heart, lung, or liver. Degradation of the glycocalyx is now considered a cornerstone in I/R-related endothelial dysfunction, which further impairs local microcirculation with a feed-forward loop of organ damage, due to vasoconstriction, leukocyte adherence, and activation of the immune response. Glycocalyx damage during I/R is evidenced by rising plasma levels of its principal constituents, heparan sulfate and syndecan-1. By contrast, the concentrations of these compounds in the circulation decrease after successful protective interventions in I/R, suggesting their use as surrogate biomarkers of endothelial integrity. In light of the importance of the glycocalyx in preserving endothelial cell integrity and its involvement in pathologic conditions, several promising therapeutic strategies to restore the damaged glycocalyx and to attenuate its deleterious consequences have been suggested. This review focuses on alterations of glycocalyx during I/R injury in general (to vital organs in particular), and on maneuvers aimed at glycocalyx recovery during I/R injury.