In order to accurately and precisely measure plasma and cerebrospinal fluid (CSF) 1-beta-D-arabinofuranosylcytosine (Ara-C) in pediatric samples with adequate sensitivity and without interference, we have developed a reversed-phase ion-pairing technique utilizing the free amino group of the pyrimidine ring of Ara-C. Optimum resolution and separation was achieved utilizing a 4 microns C18 radial compression column. Ara-C and the internal standard 8-bromo-cyclic-AMP eluted at 6.5 and 4.6 min, respectively, with complete resolution. The minimum detectable amount is 2.5 pmol in a 50-microliters volume. The assay was linear in both plasma and CSF. Intra- and inter-day assay precision were less than 4% and 9%, respectively, for plasma with similar results obtained for CSF. Neither endogenous compounds nor commonly co-administered drugs interfere. Validity for our method was supported by the successful assay of over 400 pediatric plasma and 50 CSF samples for pharmacokinetic analysis. The method offers accuracy, precision, sensitivity and efficiency for plasma or CSF Ara-C determination.