Recent advances in preparation of cells for flow cytometric analysis have enabled the sensitive detection of intracellular antigens. We have examined the utility of two color flow cytometry for the detection of minimal residual T cell acute lymphoblastic leukemia (T-ALL) using a combination of expression of the pan-T cell marker CD5 and intranuclear terminal deoxynucleotidyl transferase (TdT). CD5+TdT+ cells can be sensitively detected above background in remission bone marrows (0.03% sensitivity). Possible extension of this technique to the detection of minimal residual B-lineage ALL, acute myelogenous leukemia (AML), and non-hematologic malignancies is discussed.