Identifying surrogate markers of renal allograft outcome and biomarkers of acute and chronic graft injury is a critical issue for the transplant community. Measurement of serum creatinine and biopsy remain the current gold standards for the evaluation of renal allografts. These tests have significant limitations in predicting which patients are destined for immune tolerance or immune-mediated graft loss, and aiding in the management of long-term immunosuppression. The goal of biomarkers is to diagnose rejection early, determine prognosis and tailor immunosuppressive therapy in a noninvasive, cost-effective manner. Biomarker research has focused on primary areas of kidney injury, the tubules and the cells that infiltrate them. This article reviews biomarkers currently under investigation in the setting of renal allograft transplantation.