A microchip protocol for the capillary electrophoresis separation and electrochemical detection of thiol-containing degradation products of V-type nerve agents is described. The microchip assay relies on the derivatization reaction of 2-(dimethylamino)ethanethiol (DMAET), 2-(diethylamino)ethanethiol (DEAET), and 2-mercaptoethanol (ME) with o-phthaldialdehyde in the presence of the amino acid valine along with amperometric monitoring of the isoindole derivatives. Both off-chip and on-chip derivatization reactions have led to highly sensitive and rapid detection of the thiol degradation products. Various parameters influencing the derivatization, separation, and detection processes were examined and optimized. These include the amino acid co-reagent, reagent-mixing ratio, reaction time, injection time, separation voltage, and detection potential. The chip microsystem offers a rapid (<4 min) simultaneous detection of micromolar concentrations of DMAET, DEAET, and ME. Linear calibration plots were observed for the V-type nerve agent thiol degradation products, along with good stability and reproducibility (RSD < 8.0%). Detection limits of 5 and 8 microM were obtained for the off-chip reaction of DMAET and DEAET, respectively, following a 2-s injection. The suitability for assays of environmental matrixes was demonstrated for the determination of DMAET and DEAET in untreated tap and river water samples. The favorable analytical performance makes the new microfluidic device attractive for addressing the needs of various security scenarios.