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A capillary electrophoresis (CE) microchip with an amperometric, electrochemical detector (ECD) was developed to detect notorious environmental hormones, bisphenol A (BPA) and butyl-phenol. We developed a CE/ECD microchip which separates and detects the target analytes. Prussian blue (PB), an electrocatalyst that assists in detecting the analytes effectively, was used to modify the working electrode indium tin oxide (ITO) by the electrodeposition process. Each compound is transported by CE to the working electrode at different flow rates according to their charges and masses. Compared to the bare ITO electrode, the PB/ITO electrode is beneficial in terms of improved analytical performance, that is, enhanced sensitivity, low cost requirement, and simple construction scheme. The CE/ECD microchip with PB/ITO electrode is a promising technology for the easy detection of certain environmental hormones.