A new method for the determination of perchlorate in water and soil samples using on-line enrichment in a capillary zone electrophoresis-mass spectrometry is presented. The target analytes in the sample solutions were introduced into the capillary column by pressure-assisted electrokinetic injection (PAEKI) with the simultaneous application of -18 kV and +50 mbar external pressure to the sample vial at the capillary inlet for 4 min. The injected sample zone was flushed out with a running buffer and analyzed by a tandem mass spectrometer in a negative selected reaction monitoring mode. The influence of the matrix in both water and soil samples was eliminated by a clean-up step by passing the sample through Ba/Ag/H cartridges. The method showed good linearity in the dynamic range of 20 to 1000 ng/L, and achieved a detection limit of 18.7 ng/L for water samples and 3.3 ng/g for soil samples, respectively. The recovery of perchlorate in spiked samples, at three different levels, ranged over 79-127%. The method reproducibility was found to be 11% RSD for water samples and 7% RSD for soil samples. Perchlorate was found in 25 out of 28 water samples analyzed, with the levels ranging from 19.8 to 192 ng/L, and was not detected in the 10 soil samples analyzed.