Flow cytometry has become an essential tool for identification and characterization of hematological cancers and now, due to technological improvements, allows the identification and rapid enumeration of small tumor populations that may be present after induction therapy (minimal residual disease, MRD). The quantitation of MRD has been shown to correlate with relapse and survival rates in numerous diseases and in certain cases, and evidence of MRD is used to alter treatment protocols. Recent improvements in hardware allow for high data rate collection. Improved fluorochromes take advantage of violet laser excitation and maximize signal-to-noise ratio allowing the population of interest to be isolated in multiparameter space. This isolation, together with a low background rate, permits for detection of residual tumor populations in a background of normal cells. When counting such rare events, the distribution is governed by Poisson statistics, with precision increasing with higher numbers of cells collected. In several hematological malignancies, identification of populations at frequencies of 0.01% and lower has been attained. The choice of antibodies used in MRD detection facilitates the definition of a fingerprint to identify abnormal populations throughout treatment. Tumor populations can change phenotype, and an approach that relies on ‘different from normal’ has proven useful, particularly in the acute leukemias. Flow cytometry can and is used for detection of MRD in many hematological diseases; however, standardized approaches for specific diseases must be developed to ensure precise identification and enumeration that may alter the course of patient treatment.