Biomarkers are indispensable tools for assessing kidney allograft prognosis and kidney failure trajectory. A biomarker is defined as a characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or responses to an exposure or intervention, including therapeutic interventions. While serum creatinine level, estimated glomerular filtration rate, and albuminuria may be considered biomarkers, they are neither specific nor sensitive for assessing kidney allograft status. Molecular biomarkers are the cornerstones of personalized transplantation medicine; noninvasive biomarkers have additional advantages, including the avoidance of invasive biopsies and the convenience of serial measurements to provide a sequential assessment of the allograft and recipient’s immune status. In this chapter, we focus on the underlying principles and clinical utility of commercially available common molecular biomarkers in kidney transplantation. Using a clinical case vignette, we discuss the interpretation of single antigen bead assay for alloantibodies, donor-derived cell-free DNA testing, and immune cell function assay. While cost and availability pose significant limitations to their widespread application, promising early studies have demonstrated the feasibility of using molecular biomarkers to monitor kidney transplant recipients in India. Although no molecular biomarker is perfect, the judicious use of a combination of tests would facilitate the effective practice of individualized patient-centric transplantation medicine.