In organ transplantation, achieving an operational tolerance is the ultimate goal. However, inducing this tolerance with a minimal dose of anti-rejection drugs can only be safely achieved when guided by biomarkers reflecting the immune reactivity in patients. We review recently described biomarkers and assays for the identification of patients for their risk of organ rejection and their suitability for drug weaning. The clinical assessment of tolerance has been attempted with immunological tools, including the analysis of immune cell subsets, regulatory T cells, ELISPOT, and trans-vivo delayed-type hypersensitivity assays. These methods are promising tools for diagnosis; however, their ability to determine the presence and persistence of responsiveness to their transplant is not available. As the "omics" technologies advance, comprehensive and high-throughput biomarker studies have become more accessible, more affordable, and more customizable. Validating the use of microarray analysis has important implications for monitoring patients for the development of tolerance following transplantation as well as for determining the mechanisms by which tolerance is induced and maintained. Finally, collaborative efforts are needed to design and perform prospective multicenter trials to validate the identified biomarkers across different laboratories.