A rapid, sensitive and robust sample preparation procedure for the quantitative determination of indinavir in human cerebrospinal fluid (CSF) and plasma is described. Indinavir and the internal standard were isolated from CSF or plasma samples by cation-exchange solid-phase extraction with SCX cartridges, while the chromatographic separation was adopted from a previous method, using a cyano column connected by a switching valve to a C18 column. UV detection was set at 210 nm. The standard curve was linear over the concentration range of 2 to 2000 ng/ml in CSF and 5 to 2000 ng/ml in plasma. The intra-day coefficients of variation at all concentration levels were < or = 5.9%. The inter-day consistency was assessed by running QC samples during each daily run. The coefficients of variation for quality control samples in both matrixes were < or = 6.1%. The method has been utilized to support clinical pharmacokinetic studies.