Multiparameter flow cytometry offers the unique ability to simultaneously assess and correlate multiple cellular properties at the single cell level in a timely and efficient manner. Application of this technique to the detection of residual acute leukemia after therapy has been shown to be of singular importance to monitor response to therapy and provide prognostic information. Principles and methods that allow for the sensitive detection of acute leukemia following therapy are presented. The basic protocol outlines a simple and efficient method for the labeling of white cells with monoclonal antibodies directed against cell surface antigens. A second method describes a general method for the simultaneous assessment of surface and cytoplasmic antigens using a combination of fixation followed by membrane permeabilization. An illustrative panel of validated reagents currently in use for residual disease detection for acute lymphoblastic leukemia of B or T cell lineage as well as acute myeloid leukemia is provided. Principles of data analysis that allow for the reproducible detection of small populations of abnormal hematopoietic cells in peripheral blood and bone marrow are presented.