Abstract: Methods for diagnosing and identifying genetic and metabolic factors associated with a physiologic procoagulant predisposition for and concurrent activation of the coagulation response in patients suffering from conditions such as chronic fatigue syndrome, fibromyalgia, Gulf War illness and cardiovascular disease are disclosed. Diagnostic assays utilized in the methods include measurement of blood levels of Protein C, Protein S, antithrombin, activated protein C resistance, prothrombin, plasminogen activator inhibitor-1, lipoprotein (a) and homocysteine. Treatment regimens include anticoagulant therapies comprising administering warfarin or heparin as needed.