By simultaneous DNA staining and immunophenotyping, the aneuploid blasts of acute lymphoblastic leukemia (ALL) can be quantitated by flow cytometry. The present study evaluates the application of this method for the detection of minimal residual disease (MRD). For this purpose leukemia cells with known aneuploidy were serially diluted with diploid bone marrow cells obtained after chemotherapy. These mixed samples were immunophenotyped using antibodies CD34, CD10, or CD19 and processed for DNA staining with propidium iodide. Fifty thousand cells were measured for each experiment and the results were compared with the analysis of control sample without added aneuploid cells. Aneuploid cells diluted to 1% were not detectable in 6/15 cases when DNA content analysis was used alone, and in dilutions of < 1%, these cells were not detectable. When DNA content and immunophenotype were simultaneously measured, aneuploidy was detectable in 15/15 cases at 1.00%, 6/6 at 0.50%, 16/16 at 0.10%, and 16/17 at 0.05%. Therefore this method may be useful for the detection of minimal residual disease in cases of aneuploid lymphoblastic leukemia.