Disclosed are methods of identifying subjects with Diabetes or a pre-diabetic condition, methods of identifying subjects at risk for developing Diabetes or a pre-diabetic condition, methods of differentially diagnosing diseases associated with Diabetes or a pre-diabetic condition from other diseases or within sub-classifications of Diabetes, methods of evaluating the risk of progression to Diabetes or a pre-diabetic condition in patients, methods of evaluating the effectiveness of treatments in subjects with Diabetes or a pre-diabetic condition, and methods of selecting therapies for treating Diabetes or a pre-diabetic condition, using biomarkers.