In this study nanocrystalline hydroxyapatite (nHA) was synthesized and characterized by means of FT-IR, XRD and TEM techniques and a series of proton exchange membranes based on Nafion (R) and nHA were fabricated via solvent casting method. Thermogravimetric analysis confirmed thermal stability enhancement of the Nafion (R) nanocomposite due to the presence of nHA nanopowder. SAXS and TEM analyses confirmed the incorporation of nHA into ionic phase of Nafion (R). Furthermore, the incorporation of elliptical nHA into the Nafion (R) matrix improved proton conductivity of the resultant polyelectrolyte membrane up to 0.173 S cm(-1) at 2.0 wt% of nHA loading compared to that of 0.086 S cm(-1) for Nafion (R) 117. Also, the inclusion of nHA nanoparticles into nanocomposite membranes resulted in a significant reduction of methanol permeability and crossover in comparison with pristine Nafion (R) membranes. Membrane selectivity parameter of the nanocomposites at 2.0 wt% nHA was calculated and found to be 106,800 S s cm(-3), which is more than two times than that of Nafion (R) 117. Direct methanol fuel cell tests revealed that Nafion (R)/nHA nanocomposite membranes were able to provide higher fuel cell efficiency and also better electrochemical performance in both low and high concentrations of methanol feed. Thus, the current study shows that nHA enhances the functionality of Nafion (R) as fuel cell membranes. (C) 2010 Elsevier Ltd. All rights reserved.