A chemically modified electrode has been developed as a detector for the sensitive and selective determination of thiol-containing compounds following capillary electrophoresis separation. Electrodes were constructed by entrapment of the coenzyme pyrroloquinoline quinone (PQQ) into a polypyrrole (PPy) matrix on a 245-microm graphite electrode during electropolymerization of pyrrole in the presence of PQQ. PQQ serves as an efficient biocatalyst to mediate the oxidation of thiols at a substantially reduced overpotential relative to an unmodified electrode. Furthermore, this design takes advantage of the pH-dependent reversible electrochemical properties of PQQ, which facilitates optimization of separation and detection conditions. The PQQ/PPy-modified electrode was incorporated as an end-column detector, and a separation of homocysteine, cysteine, N-acetylcysteine, and glutathione was developed. Detection limits for these four thiols were determined to be 11, 23, 104, and 134 nM, respectively, with mass detection limits ranging from 0.29 to 3.48 fmol. The PQQ/PPy electrode was also found to be very reproducible in run-to-run, day-to-day, and electrode-to-electrode comparisons. The utility of this electrode was demonstrated for the detection of cysteine in dietary supplements and human urine, resulting in excellent agreement with reported values.