Allogeneic stem cell transplantation (allo-SCT) is an effective and potentially curative treatment for some cases of multiple myeloma (MM). The curative efficacy of allo-SCT may be largely attributed to its immunological activity, the graft-versus-myeloma (GVM) effect. To evaluate the kinetics of residual myeloma cells, we analyzed the follow-up bone marrow samples of three MM patients by means of a real-time molecular assay. We identified a consistent correlation between onset of graft-versus-host disease and disease response. These data suggest that real-time molecular follow-up can be used to monitor the GVM effect and that it can be employed in the clinical setting to tailor post transplant immunomodulation.