We have isolated and characterized two forms of soluble thrombomodulin from human urine. The purification procedure consisted of ultrafiltration, chromatography on DEAE-Sepharose, affinity chromatography on diisopropyl-phosphate -thrombin and/or monoclonal anti-thrombomodulin IgG affigel followed by reverse-phase HPLC. An active soluble form of thrombomodulin was purified 1600-fold from 34-1 urine. The purified protein migrated as a doublet, with molecular mass 761 72 kDa under reducing conditions and 63/57 kDa under non-reducing conditions as determined by SDSPAGE. Amino acid analysis of the 63/57-kDa soluble thrombomodulin confirmed sequence identity with human thrombomodulin and demonstrated N-terminal heterogeneity. Compared to membrane-type thrombomodulin, the purified 63/57-kDa soluble thrombomodulin was more active as a cofactor for protein-C activation. The second major thrombomodulin fragment in urine is an inactive 35-kDa thrombomodulin polypeptide derived from the N-terminal extracellular region of thrombomodulin.Thrombomodulin is an endothelial cell-surface glycoprotein which forms a high-affinity non-covalent complex with thrombin. In this complex, thrombomodulin acts as a cofactor for thrombin in the activation of protein C, enhancing the reaction rate by greater than 1000-fold to form activated protein C. Activated protein C acts as a natural anticoagulant by proteolytic degradation of factors Va and VIIIa [ l , 21. Thrombomodulin is a single-chain 554-residue integral membrane protein comprising a signal peptide, an N-terminal domain, six epidermal-growth-factor-like repeats, an O-glycosylation-rich domain followed by a transmembrane segment and a short cytoplasmic tail [3]. The protein has been isolated from rabbit [2], bovine lungs [4] and human placenta [5]. The molecular and functional characteristics of membrane thrombomodulin have been well delineated [6, 71. Cell-surface expression of thrombomodulin is regulated by a number of mechanisms including a tumour-necrosisfactor-mediated process which regulates transcription of the thrombomodulin gene [ 81, internalization by receptor-mediated endocytosis [9] and proteolytic cleavage from the endothelial cell membrane [lo]. The relative role of each of these mechanisms in the surface expression of thrombomodulin has yet to be defined.Previous studies have identified the presence of molecules in plasma and urine that are immunologically indistinguishable from membrane thrombomodulin [ 111. Some of these molecules act as thrombin cofactors in the activation