Involvement of the cerebrospinal fluid (CSF) by hematopoietic malignancies may be difficult to document by morphology alone. The diagnoses of "atypical" or "suspicious" is frequently used in cases with low numbers of cells or ambiguous morphology. In a study comparing morphology alone to morphology with flow cytometry, we demonstrated that flow cytometric immunophneotyping was useful in establishing a diagnosis of neoplasia in a series of patients with known lymphoma or leukemia and an initial diagnosis of "atypical" or "suspicious" CSF using morphologic criteria. The Flow Cytometry Unit evaluated the role of flow cytometric analysis in staging and management of patients with high grade B cell lymphomas. We assessed the cerebrospinal fluid (CSF) by flow cytometry and cytology in patients newly diagnosed with aggressive B-cell lymphomas and at risk for central nervous system (CNS) involvement. Flow cytometry identified neoplastic clones that constituted as little as 0.2% of total CSF lymphocytes. Flow cytometry detected involvement where cytology, chemistry and cell counts failed. Flow cytometric detection of disease was a negative prognostic factor and now prompts therapeutic intervention in patients on NCI protocols. As a result of the study we recommended that patients at risk for CNS involvement by aggressive B cell lymphoma undergo staging CSF evaluation by flow cytometry. Many flow cytometry laboratories report a low success rate in analysis of CSF specimens. The Flow Cytometry Unit, CCR, NCI, NIH developed special protocols for flow cytometric analysis of CSF that has led to a high success rate. The Flow Cytometry Unit participated in an international consensus conference to determine optimal methodology for flow cytometric analysis of CSF. The consensus recommendations are in press in Current Protocols in Cytometry.