An analytical test procedure for the direct determination of trace levels of perchlorate in drinking water by isotachophoresis combined with capillary zone electrophoresis was developed. A capillary electrophoresis analyzer with column coupling technology, capable of combining capillaries with different internal diameters, was employed in combination with conductivity detection. This combination of the capillary electrophoresis techniques facilitated preconcentration of the trace analytes and elimination of potentially interfering macro-components. To eliminate the influence of weak and moderately strong acids on the migration of perchlorate, acidic leading electrolyte (pH 3.2) in the isotachophoresis step and acidic background electrolyte (pH 3.9) in the zone electrophoresis step were chosen. The addition of polyvinylpyrrolidone into the electrolytes enhanced the resolution of perchlorate from other anions, especially remaining anionic macro-components. The developed method is characterized by good repeatability of migration time (relative standard deviation less than 0.2%) as well as peak area (relative standard deviation less than 5.9%), linearity (R = 0.9996), recoveries (100-112%), and sample throughput (90 samples/24 h). The limit of quantitation for perchlorate in drinking water was achieved at 12.5 nmol/L (1.25 μg/L). This approach is more sensitive and more robust than transient isotachophoresis and offers advantages over some more established analytical techniques such as ion chromatography.