In this work, we describe a novel electrochemical detection method, differential pulsed amperometry (DPA) on microchip capillary electrophoresis (MCE). In a pulse period, a sequential two-step sampling is executed at two different potentials (E-1 and E-2). Differential current signal of the duplex sampling events is recorded that functions as time domain. The performance of this detection scheme was evaluated by separating and detecting three model analytes including tyramine (Tym), tryptophan (Trp), and p-aminobenzoic acid (PABA). Multiple parameters that would affect electrochemical response and peak shape, such as sampling potential, sampling time, and electrode cleaning time, were investigated. This pulse technique exhibits better sensitivity over constant potential amperometry (CPA), nearly equal to triple pulsed amperometry (TPA). More importantly, DPA can generate more stable baseline than TPA, primarily due to the background subtraction through the two-step sampling, which is beneficial to further improve analytical sensitivity. In the optimal condition, the limits of detection for Tym, Trp and PABA, were down to 0.27 mu M, 0.32 mu M and 1.1 mu M, respectively. DPA detection opens up a new avenue for microchip electrochemistry, and can be virtually extended to other fluid analysis techniques. (C) 2013 Elsevier B.V. All rights reserved.