The examination of cerebrospinal fluid (CSF) continues to play an important role in the diagnosis of inflammatory diseases of the central nervous system (CNS). Immunocytochemistry and flow cytometry are the most commonly used methods for analysis of surface markers on CSF cells. We here compared these methods in the examination of CSF cells from a total of 68 patients with acute and chronic inflammatory CNS diseases. Expression of costimulatory molecules CD80 (B7‐1) and CD86 (B7‐2) as activation markers that are present at low density on the cell surface was analyzed in comparison to CD22 (B‐cells) and CD4 (T‐cell subset), that show high staining intensities. For CD22 and CD4, the results obtained with both methods were similar and reliable. Using flow cytometry, CD80 expression was detected in 6% of CSF cells in patients with chronic inflammatory CNS disease, as compared to 2% using immunocytochemistry, where the reliability of the data was found to be higher. We conclude that for examination of low‐density surface markers on CSF cells, particularly with low cell counts, immunocytochemistry may be more reliable. Diagn. Cytopathol. 1999;21:313–318. © 1999 Wiley‐Liss, Inc.