PURPOSE: To obtain a thrombomodulin composition which can prevent the components from polymerizing during the lyophilization.

CONSTITUTION: This thrombomodulin composition contains thrombomodulin and 0.01 to 1mmol, per 1mg of thrombomodulin, of at least one selected from the group of amino acids or their salts and saccharides. The amino acids and their salts are, for example, arginine, glutamic acid, proline, serine, glycine, histidine, asparagine, lysine, phenylalanine and valine and their salts, while the saccharides are, for example, mannitol, trehalose, lactose or sucrose. Thrombomodulin has anti-coagulant, platelet-agglutination suppressing action, and thrombolytic actions and is expectedly used for treatment and prevention of diseases such as myocardial infarction, thrombosis, embolism, peripheral vascular obstruction, arteriosclerosis obliterans, disseminated intravascular coagulation, stenocardia, transient ischemic attack or toxemia of pregnancy.