Among the most thoroughly evaluated modalities for assessment of minimal residual disease (MRD) in B acute lymphoblastic leukemia is multiparameter flow cytometry. Flow cytometric evaluation of MRD for B-ALL requires complete understanding of the immunophenotype of hematogones, the normal counterpart of leukemic B lymphoblasts. Assessment of multiple flow cytometry markers, in concert with each other in multidimensional histograms, is necessary to distinguish hematogones from malignant blasts. Emerging therapies targeting CD19 and other B-cell markers can disrupt the most frequently MRD assessment, requiring a revised approach as use of targeted therapies becomes widespread.