Methods are provided for diagnosing and/or characterizing chronic immune disease activity in a subject. In the subject methods, a sample is obtained from a subject suspected of having or known to have a chronic immune disease. The sample is then assayed for the presence of native Stat-1 protein and/or any lower molecular weight fragments of Stat-1 protein present. The assay results are used to diagnose the presence of chronic immune disease activity and/or characterize chronic immune disease activity in the subject, e.g., to confirm an initial chronic immune disease diagnosis, to determine the stage of the disease, to monitor disease progression, to predict disease attacks, and the like. In certain embodiments, the assay results are also used to predict the effectiveness of a particularly treatment protocol, e.g., to determine whether an interferon based treatment protocol will be effective. In addition, methods of Stat-1 based methods of treating chronic immune disease conditions are provided. Also provided by the subject invention are kits for practicing the methods.