There is burgeoning evidence that branch chain amino acids (BCAAs) are biomarkers of metabolic, cardiovascular, renal and cerebrovascular disease. The purpose of this review is to summarize the current evidence in this area. Recent evidence demonstrates that BCAAs are associated with insulin resistance, type 2 diabetes, risk of cardiovascular disease, stage I and II chronic kidney disease and ischemic stroke. Further, circulating levels of BCAAs have the potential to predict populations at risk for cardiometabolic disease, type 2 diabetes and mortality from ischemic heart disease. Importantly, the relationship of BCAAs to insulin resistance is affected by the intake of fat in the diet as well as age. Current evidence supports the potential use of BCAAs as biomarkers of disease. However, questions regarding the mechanisms underlying the relationship of BCAAs to disease process and severity need to be answered prior to the use of BCAAs as a biomarker in clinical practice.