Within the last 25 years, flow cytometry and fluorescence-activated cell sorting have emerged as both routine diagnostic tools in clinical medicine and as advanced analytic tools critical in performing scientific research. This chapter aims at summarizing the use of flow cytometry in benign and malignant hematology and the monitoring of inherited and acquired immunodeficiency states. Numerous figures are provided from our laboratories at Massachusetts General Hospital that illustrate examples of these conditions. The chapter also describes novel flow cytometry-based imaging techniques, the combination of flow cytometry and mass spectrography, new software tools, and some future directions and applications of advanced instrumentation for flow cytometry.