A vexing problem after hematopoietic cell transplantation (HCT) for leukemia is assessing the biologic significance of low numbers of cells "suspicious" for relapse seen in morphologic review of peripheral blood smears (PBSs). In 27 patients, in apparent hematologic remission after HCT for leukemia, we studied the nature of such cells in PBSs to the endpoint of leukemic relapse by using multidimensional flow cytometry (MDF) on blood or bone marrow aspirates. Based on abnormal cytometric maturational patterns, +/- cell sorting of blasts with fluorescence in situ hybridization with informative markers, we differentiated benign recovering myeloid and lymphoid precursors from leukemic cells. In 17 patients, blasts were characterized by MDF as normal early hematopoietic precursors, lymphoblasts, or NK cells. Of these patients, 16 remained in remission for at least 42 days. In 10 patients, blasts were characterized by MDF as a malignant immunophenotype; 9 relapsed within 10 days and 1 relapsed 280 days after a graft-vs-leukemia effect. MDF status was strongly associated with a 90 x probability of relapse even after adjusting for other potential variables. Morphologic triggered MDF characterization of peripheral blasts is a powerful and rapid tool for distinguishing immature regenerative forms from early leukemic relapse.