Nowadays, polymer electrolyte membrane fuel cells (PEMFCs) and direct methanol fuel cells (DMFCs) are devices known for using proton conducting membranes. From a conceptual point of view, DMFC and PEMFC systems are very similar, except for being supplied by different fuels such as methanol and hydrogen, respectively. Commonly, PEMFCs are performed at temperature lower than 100 degrees C owing to the failure of the electrochemical performances of Nafion. Nevertheless, taking into account the poisoning effect of CO on the fuel cell catalyst (conventionally based on Pt), the ideal working temperature of the PEMFCs should be above 100 degrees C, where CO poisoning could be drastically reduced or avoided. Today, Nafion is recognized as the most used proton exchange membrane in the market, useful for both PEMFC and DMFC applications. It is based on a perfluorinated polymer and shows good thermal stability and high proton conductivity as main benefits. On the contrary, Nafion is an expensive material and suffers high fuel crossover (particularly, methanol crossover in DMFC applications) besides the proton conductivity loss above 100 degrees C. Therefore, in the last decades many scientists paid special attention on the development of new materials based on non-fluorinated polymers as an alternative to Nafion. One of the most promising class of is represented by the polyetheretherketone (PEEK). According to the specialized literature, interesting performances in terms of proton conductivity and thermo-chemical properties as well as low fuel crossover and costs are noticeable for sulfonated PEEK-based polymers. Indeed, many scientific applications are devoted to modify PEEK polymer for manufacturing membranes alternative to Nafion for both PEMFC and DMFC applications. Among them, important methods are exploited for preparing electrolyte membranes from PEEK such as: a) PEEK electrophilic sulfonation (S-PEEK); b) S-PEEK and non-functional polymers blending; c) S-PEEK, heteropolycompounds and poly-ether-imide doping with inorganic acids, etc. In this review, the potentialities of PEEK-based polymers are discussed, pointing out the main benefits and drawbacks of these proton exchange membranes for fuel cell applications. As a case study, the use of sulfonated PEEK with cardo-group (PEEK-WC) is particularly stressed, pointing out the main characteristics for its applications in PEMFCs and DMFCs as an alternative to Nafion membrane. Copyright (c) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.