Previous studies to evaluate minimal disease in acute lymphoblastic leukemia (ALL) after treatment have relied on the diagnostic specimen to develop patient-specific analytical probes. The diagnostic specimen is often not available in a tertiary setting; therefore, we evaluated the use of flow cytometry (FCM) using a “difference from normal” approach to detect residual disease prior to myeloablative allogeneic hematopoietic cell transplantation (HCT). Among 116 pediatric patients with ALL who were in morphological remission at time of transplant, we found that those patients who had detectable residual disease by FCM prior to HCT experienced significantly inferior outcome. Pediatr Blood Cancer 2011;57:163–165. © 2011 Wiley-Liss, Inc.