Immunosuppressive drug level monitoring and serum creatinine are widely used for kidney transplantation (KT) monitoring. Monitoring of drug level is not the direct measurement of the immune response while the rising of creatinine is too late for detection of allograft injury. Kidney biopsy, the gold standard for KT monitoring, is invasive and may lead to complications. Many biomarkers have been discovered for direct monitoring of the immune system in KT and the benefit of some biomarkers has reached clinical level. In order to use biomarkers for KT monitoring, physicians have to understand the biology including kinetics of each marker. This can guide biomarker selection for specific condition. Herein, we summarize the recent findings of donor specific anti-human leukocyte antigen antibody, B lymphocyte stimulator, interferon-gamma induced protein of 10 kDa, and intracellular adenosine triphosphate monitoring, all of which have very strong evidence support for the clinical use in KT.