Traditionally described as a major anti-coagulant system, the protein C (PC) pathway, consisting of thrombomodulin, the endothelial cell protein C receptor and activated PC (APC), is gaining increasing attention as an important regulator of microvascular inflammation. Although they possess several anti-inflammatory and cytoprotective functions, the expression and function of the components of the PC pathway is downregulated during inflammation. Recent evidence suggests that the PC pathway is defective in patients with inflammatory bowel disease (IBD) and that restoring its function has anti-inflammatory effects on cultured intestinal microvascular endothelial cells and in animal models of colitis. Here, we propose that the PC pathway has an important role in governing intestinal microvascular inflammation and might provide a novel therapeutic target in the management of IBD.