Clinical use of valid biomarkers enables the prediction of alloreactive response (risk of rejection) and personal susceptibility to immunosuppressive treatment could lead to personalized immunosuppressive therapy. In clinical transplantation, it has been reported that cytokine production and secretion could be modified by immunosuppressive drugs, as well as during the rejection process. Some cytokines such as interferon (IFN)-γ, interleukin (IL)-2, IL-10, and transforming growth factor (TGF)-β have been identified as candidate biomarkers that correlate with graft outcome and personal response to immunosuppressive agents. This review will focus on the current state of knowledge, indicating that monitoring changes in cytokine production could be used to predict the risk of rejection and to guide immunosuppression therapy in transplant recipients. In addition, many questions regarding the characteristics and standardization of the methods used for cytokine monitoring (ELISA; ELISPOT; Flow Cytometry) that need to be addressed before these assays can be clinically applied will be discussed in light of recent studies showing an association between the expression of some cytokines and genetic variants, the impact of immunosuppression, and the incidence of rejection. The clinical implementation of cytokine monitoring should be tested in prospective multicenter clinical trials with standard operating procedures and objective interpretation of the results obtained.