We analyzed minimal residual disease (MRD) by multidimensional flow cytometry (MFC) after allogeneic stem cell transplantation in 41 patients with acute myeloid leukemia (AML) (n = 31) or acute lymphoblastic leukemia (ALL) (n = 10). Aberrant antigen expression was compared with the results of quantitative PCR for WT1 mRNA (n = 41) and leukemia-specific fusion transcripts (n = 12; AML in seven, ALL in five). There was a significant correlation between detection of MRD by MFC and WT1 mRNA, as well as between MFC and fusion transcripts. Serial monitoring of MRD by the three techniques correlated in parallel to the clinical course in most of the patients, but three patients were only positive for WT1 during hematological remission. The overall survival time of patients with complete remission was significantly associated with the appearance of aberrant expression after transplantation. In conclusion, MFC is valuable for clinical management decisions after transplantation. (C) 2012 Elsevier Ltd. All rights reserved.