Organ transplant recipients are at risk of allograft rejection, and remain dependent on lifelong immunosuppressive agents, with the attendant risks of infections, cancers, and drug toxicities. Mesenchymal stromal cells (MSCs) have emerged as an alternative to the current pharmacologic immunosuppressive therapy as these cells are immune privileged and possess immunomodulatory properties. However, clinical data are incomplete regarding the efficacy of MSC therapy to control alloimmune response of the transplant recipients. Coordinated efforts should now be directed towards assays for monitoring anti-donor T cell response of MSC-treated patients to establish the pro-tolerogenic potential of MSC-based therapy. Here, we describe two useful tools to monitor MSC-mediated immunomodulation: the assessment of T cell proliferation by carboxyfluorescein succinimidyl ester (CFSE) dilution assay and the evaluation of cytotoxic T lymphocyte (CTL)-mediated lysis of (51)Cr-labeled target cells (cell-mediated lympholysis; CML) following mixed lymphocyte cultures of peripheral blood mononuclear cells (PBMCs) from kidney donors and transplant recipients.