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The urokinase plasminogen activator (uPA), a serine protease, binds to its cellular receptor, the urokinase plasminogen activator receptor (uPAR), with high affinity and initiates a number of cascades leading to extracellular matrix remodeling,activation of other proteases, and intracellular signaling.The urokinase plasminogen activator system has been implicated in a number of pathological processes including tumor growth, metastasis, and inflammation.We described here two crystal structures in this system: 1) uPAR complexed with the amino terminal fragment ofuPA (ATF), which contains the uPAR binding domain, at 1.9 (A) resolution; 2) uPA complexed with a cyclic peptidyl uPAinhibitor that is highly specific to uPA.These structures present a framework to further develop or optimize antagonists to intervene uPA-uPAR system and its pathophysiological consequences.