AbstractSensitivity is a crucial point in the development applications for medicine or environmental samples in which the analytes are present in the nanomolar range. Besides further technical development of detection systems, the multiplex sample injection technique can be applied for enhancing the signal‐to‐noise ratio. Hadamard transform is easily applied to microchip electrophoresis due to the fact that sample injection is generally achieved through cross, double‐tee, or tee injector structures. This paper reports the first demonstration of a modified Hadamard transform electrophoresis on a microchip by using an amperometric detector. Contrary to the previous Hadamard applications, the resolution (number of points per unit of time) of electropherograms obtained is independent of the number of injections.