A simple, automated system for the determination of trace perchlorate by ion chromatography (IC) with an online preconcentration technique is reported. The sample is preconcentrated, and less strongly held ions preeluted before the analyte is transferred to the principal separation system. This approach provides low limits of detection (LOD) and is particularly robust toward the effect of high concentrations of common anions, such as those present in groundwater samples. It compares favorably with currently promulgated EPA method 314.0. The LOD (S/N = 3) is 0.77 μg/L for a 2-mL reagent water sample and decreases more-or-less proportionately with increasing sample volume, at least up to 20 mL. Even with a sample of conductivity 14.7 mS/cm (approximately that of 0.1 M Na2SO4), the recovery of added perchlorate at the 25.0 μg/L level was still 92%. The concentration of added perchlorate in the range of 1-400 μg/L was linearly correlated to the peak area, with an r2 value of 0.9997. The recovery of perchlorate from artificial samples with different conductivity by the present method compares favorably with those from the currently recommended EPA Method. The ability of this approach to remove matrix interferences suggests that it would be also promising for perchlorate analysis in other challenging samples.