Sepsis is the third largest cause of death in industrialised countries, but treatment remains largely supportive and effective therapeutic interventions are urgently needed. Disruption and dysfunction of the microvascular endothelium leading directly or indirectly to multiple organ failure are now recognised to underpin the pathophysiology of sepsis. Biomarkers of endothelial activation may therefore assume an important role in guiding future research efforts. We suggest that integral to this approach is the investigation and evaluation of endothelial glycocalyx biomarkers, not only as indicators of the pathogenic process but also to inform the development of pharmacological and other therapies.