Pulsed electrochemical detection (PED) following capillary electrophoresis (CE) has been applied to the direct detection of thiocompounds. Both reduced and oxidized thiol moieties are detected without the need of derivatization. Thiocompounds can be detected over a wide range of pH conditions (i.e., pH 0-14), and except for pH, their response is relatively unperturbed by buffer composition. Integrated pulsed amperometric detection (IPAD) results in more stable baselines, eliminates oxide-induced artifacts, and yields lower limits of detection than other PED waveforms. Mass detection limits using optimized IPAD waveforms are typically 2 pg (5 fmol) or less. The high selectivity of PED for thiocompounds reduces sample preparation and produces simpler electropherograms of complex samples containing these biologically significant compounds.