Collection of cerebrospinal fluid (CSF) from the lumbar subarachnoid space is a routine procedure in clinical neurology, providing an opportunity to obtain hematogenous cells from the central nervous system environment in vivo. The ability to study individual cells in samples with low cell numbers has made flow cytometry an attractive method for studies of chemokine receptor expression on such cells. Several methodological variables such as staining temperature and cell isolation techniques may, however, influence the final outcome of the staining. In addition, low numbers of cells in the normal lumbar CSF, together with a tendency of CSF cells to decay rapidly after sampling, require meticulous handling of the samples. Here, we describe the methodology used in our laboratory to study chemokine receptor expression on cells in paired samples from peripheral blood and CSF using flow cytometry.