Flow cytometry has applications in numerous fields, including molecular biology, protein engineering, pathology, immunology, plant and marine biology. The identification and quantization of cellular antigens with fluorochrome labeled monoclonal antibodies (Immunophenotyping) is one of the most important applications of the flow cytometer.

Immunophenotypic analysis is critical to the initial diagnosis and classification of the acute leukemias, chronic lymphoproliferative diseases, and malignant lymphomas since treatment strategy often depends upon antigenic parameters.
In addition, immunophenotypic analysis provides prognostic information not available by other techniques, provides a sensitive means to monitor the progress of patients after chemotherapy or bone marrow transplantation, and often permits the detection of minimal residual disease. Flow cytometric analysis of apoptosis, multidrug resistance, leukemia-specific chimeric proteins, cytokine receptors and other parameters may provide additional diagnostic or prognostic information in the near future.