The detection and quantification of minimal residual leukemia (MRD) has importance for monitoring continued disease response and detection of early relapse. We retrospectively compared MRD detection rates and percentages of residual leukemia by flow cytometry immunophenotyping (FCIP) with results obtained by either flow cytometry DNA (FCDNA) ploidy (n = 14) and/or fluorescent in situ hybridization (FISH) (n = 33) testing for cases with 1.5% or less residual leukemia. A total of 42 paired results were obtained from 20 pediatric patients, including 16 with B lineage acute lymphocytic leukemia and 4 patients with acute myeloid leukemia during the course of induction and/or relapse. Eighty-one percent of the results were concordant (20 negative and 14 positive). There was reasonable correlation coefficients for quantity of residual disease by FCIP and FCDNA ploidy, and poor correlation coefficients for levels of residual disease between FCIP- and FISH-based results. FCIP MRD sensitivity and specificity was 78% and 83%, respectively. Factors contributing to the 19% discordant rate include low sensitivity of the DNA-based methods as applied and antigenic modulation of immunophenotype during the course of treatment. There is a reasonable agreement between the FCIP and FCDNA or FISH methods for detecting and quantifying MRD. However, the methods are viewed as complementary with their own inherent limitations.