Electrochemical Impedance Spectroscopy (EIS) is a widely used tool for detecting degradation phenomena in electrochemical systems. In this paper a new approach for the fast estimation of fuel cell impedance is described. It is based on the use of a Pseudo-Random Binary Sequence as perturbation signal and the application of a Fast Fourier Transform algorithm to calculate the voltage and current harmonics in the frequency domain. With respect to the other approaches shown in literature, it is more suitable to run on an embedded system, thus allowing to perform the on-line diagnosis of fuel cell systems. The digital implementation of such method on a low cost FPGA device has been also proven.