Thrombomodulin is an endothelial cell membrane protein that is a cofactor required for the rapid activation of plasma protein C. We now report that plasma and urine of normal subjects contains a modified form of thrombomodulin that is soluble. The levels measured by radioimmunoassay were 292 +/- 60 ng thrombomodulin/ml plasma and 102 +/- 38 ng thrombomodulin/ml urine. Thrombomodulin was isolated from both plasma and urine by immunoaffinity chromatography using a polyclonal anti-human thrombomodulin IgG column. The apparent molecular weight of soluble thrombomodulin was estimated by immunoblot analysis using 125I-monoclonal anti-thrombomodulin IgG. When run without 2-mercaptoethanol, soluble thrombomodulin appeared as two polypeptides, Mr = 63,000 and 54,000, while samples run with 2-mercaptoethanol migrated mainly at Mr = 85,000. These results imply that the soluble form of thrombomodulin is smaller than the cellular form, presumably because of a lack of the membrane-binding domain. Soluble thrombomodulin is similar to cellular thrombomodulin in its intrinsic protein C-activating cofactor activity as measured by antibody neutralization. The apparent Km for protein C was the same for cellular and soluble thrombomodulin, while the soluble form requires a higher concentration of thrombin (three- to fivefold) for one-half maximal activity than the cellular form. Thrombomodulin functional activity cannot be directly measured in plasma because of some inhibitory substance(s). The physiological significance of circulating and urinary thrombomodulin is presently obscure.