Relapse is the major complication after allogeneic stem cell transplantation (SCT) for acute lymphoblastic leukemia (ALL) in children. Since it has been possible to measure minimal residual disease (MRD) by real-time quantitative polymerase chain reaction, this parameter is used more frequently in the treatment of ALL. In this article, the role of MRD and chimerism in the treatment and monitoring of pediatric transplantation recipients is described. Pre-SCT MRD levels can predict the risk of relapse and can thus be used to adjust treatment. Post-SCT MRD levels and changes in chimerism can predict relapses as well, although not many treatment options are available today, except relying on a graft-versus-leukemia effect mediated by graft-versus-host disease. Finding new treatments will be the challenge for the near future.