Use of a square-wave potential program for time-dependent amperometric detection of analyte zones in capillary electrophoresis (CE) is described. Electrochemical detection for CE requires that the separation field be isolated from that of the electrochemical detection. This is generally done by physically separating the CE separation field from that of the detection. By applying a time variant potential program to the detection electrode, the detector current has a time dependence that can be used to help isolate the electrochemical detection current from that of the separation. When using a 20 μm inner-diameter capillary, we find that a square-wave potential program decreases the RMS baseline current from 4.5×10−10 A, found with a constant potential amperometric detection, to 1.1×10−10 A when using a square-wave potential program. With a 75 μm inner-diameter capillary, the improvement is even more dramatic, from 2.3×10−9 A with amperometric detection to 2.06×10−10 A when using a 1 Hz square-wave potential program. When not using the time-dependent detection with the 75 μm capillary, the analyte zones were beneath the S/N for the system and not detected. With the square-wave potential program and time-dependent detection, however, the analyte zones for an electrokinetic injection of 200 μM solution of 2,3-dihydroxybenzoic acid were observed with the 75 μm inner-diameter capillary. The improvement in the ability to discriminate the analytical signal from the background found experimentally is consistent with modeling studies.