Outcomes for patients with hematologic malignancies who experience overt relapse after allogeneic hematopoietic stem cell transplantation (HCT) are poor. There are limited data on outcomes of post-transplant minimal residual disease (MRD). In this single institution, retrospective cohort analysis of children with acute leukemia and myelodysplastic syndrome we document the pattern of relapse with a primary focus on outcomes of post-transplant MRD. Forty of 93 (43%) patients who underwent a first allogeneic HCT and who all had systematic pre and post-transplant MRD evaluations at +30, +60, +90, +180 days and at +1 and +2 years post-transplant, experienced relapse. The median time to relapse was 4.8 months post-transplant with a median survival of 4 months post-relapse. Despite frequent, systematic, routine post-HCT disease restaging evaluation, 31 patients (78%) presented with overt disease at the time of relapse. 7 patients with acute leukemia who had post-transplant MRD, presented at a median of 1 month post-transplant. Due to rapid disease progression or treatment-related mortality (TRM), there was no improvement in survival for those patients whose leukemia was detected in a state of MRD post-transplant. Our results suggest that early intervention strategies targeting post-transplant MRD for relapse prevention in acute leukemia may not be feasible.