Electromagnetic Interference induced by 50/60 Hz power line is a major problem in physiological measurements. Conventional methods using embedded software are time-consuming and require a great amount of calculations. In this paper we present a digital filter based on hardware acceleration. The design was based on ASIC that incorporated a reconfigurable Fast Fourier Transform (FFT) unit, a licensed ARM7TDMI IP hardcore and several peripheral IP blocks. Comparing with other methods, this design achieved satisfactory results in the low-frequency range, which is suitable for physiological signals acquisitions. Our method is remarkably faster than conventional methods. The simulation and experimental results confirmed the accuracy and efficiency of the proposed method.