To realize the commercialization of proton exchange membrane (PEM) fuel cells, durability and reliability remain big challenges. This paper aims to develop a fault detection, identification and analysis methodology based on a commercial fuel cell system. Effect of air stoichiometry is studied using electrochemical impedance spectroscopy (EIS). Relevant faults are: oxygen starvation, water flooding and drying. Based on the EIS measurements, a non-model based methodology is proposed consisting of four parts: feature extraction based on the spectra, feature selection, fuzzy clustering and fault analysis. Validity of the proposed diagnostic methodology is verified experimentally.