Background Cerebrospinal fluid (CSF) can be collected into ethylenediaminetetraacetic acid (EDTA) or plain tubes. The EDTA content presumably contributes to a better cell preservation. EDTA, however, is reported to cause a false elevation in the total protein concentration and to dilute the CSF sample, thereby affecting the diagnostic interpretation. To the authors’ knowledge, no validated studies support this view. The aim of this study was therefore to determine if the choice of tube (EDTA or plain) influences the results of the standard CSF analysis. Results Thirty-two paired EDTA stabilised and plain CSF samples were included. There was no statistically significant difference in the semi-quantitative protein concentrations when comparing CSF samples from EDTA and plain plastic tubes (P > 0.99). The total nucleated cell count did not differ significantly between EDTA and plain tube samples (P = 0.85). There were no significant differences in the differential cell counts between the two tubes when evaluating polymorphonuclear cells (P = 0.90), lymphocytes (P = 0.84) and monocytes/macrophages (P = 0.86). Also, there was no significant difference in the preservation of cell morphology when evaluating cytological preparations from EDTA stabilised and plain tube samples (P = 0.45). Conclusions The collection of CSF into EDTA tubes does not influence the result of the standard CSF analysis. However, a presumed positive effect of EDTA on cell preservation could not be shown in the present study.