In recent years we have seen a dramatic evolution of therapeutic approaches in the management of acute leukemia with hematopoietic stem cell transplantation (HCT). For both acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), alloHCT provides the best chance of long-term disease-free survival for significant subsets of patients. During this interval, we have witnessed an evolution of HCT from a therapy based on high-dose conditioning to our current understanding that its success depends both on cytoreduction and graft-versus-leukemia (GVL) effects mediated by adoptively transferred donor immune cells. Improvements in conditioning, infectious disease monitoring and management, histocompatibility testing and graft selection have successively improved outcomes, primarily due to a reduction in non-relapse mortality. Unfortunately, disease relapse remains a significant cause of treatment failure in both AML and ALL. Here, two distinguished experts, Prof. Charles Craddock and Prof. Dieter Hoelzer, reflect on the significant challenge of disease relapse following allogeneic HCT for AML and ALL, respectively. This is a review of the biology, current approaches, and future directions in the field and reflects concepts that were presented at the Third International Workshop on Biology, Prevention, and Treatment of Relapse after Stem Cell Transplantation held in Hamburg, Germany in November 2016 under the auspices of the EBMT and the ASBMT.