The use of flow cytometry in veterinary diagnostics is becoming a valuable clinical tool with a broad range of applications. Physical characteristics of cells can be determined by the flow cytometer laser and electronics through the measurement of changes in light scatter properties. Other components and functions of cells can be defined through the application of fluorochrome dyes that have an affinity for cellular components. Traditionally, common clinical applications are immunophenotyping of cells of the hemato-poietic system with fluorescent-labeled antibodies raised against specific cell surface proteins. Other approaches have been used to elucidate changes in cell function and DNA content. This review is intended to provide the reader with the fundamental uses of flow cytometry. Examples of clinical applications in equine patients include immune-mediated hemolytic anemia, immune-mediated thrombocytopenia (IMT), chronic inflammatory disease, and neoplasia.