A molecular dynamics simulation model has been developed and used to investigate the microscopic transport mechanism and various physical properties in an electrolyte for polymer electrolyte fuel cells. It has successfully reproduced experimental results of diffusion coefficients of positive ions and water molecules in the polymer electrolyte, which are one order of magnitude smaller than those in aqueous solutions, and of O-H vibration spectra having higher frequencies than in liquid water. The low diffusivity in the polymer electrolyte is due to polar particles forming a disordered heterogeneous structure of the hydrophilic region, which constitutes the transport paths for ions and water molecules. About 25% of the positive ions are dissociated from sulfonate anions at the ends of side chains in the hydrated electrolyte and move sequentially from one sulfonate anion to the other in the vicinity of 0.5 nm about two or three times per nanosecond. This transport mechanism of ions means that the main constraining factors for ion transport in the polymer electrolyte are coulombic interactions from the sulfonate anions and tortuosity of the hydrophilic region. Based on the results, guiding principles to enhance ion diffusivity in the polymer electrolyte are proposed.Polymer electrolyte fuel cells ͑PEFCs͒ are one of the most promising kinds of energy equipment and are a core technology of hydrogen energy systems. 1 Although their utility as a power supply for vehicles is common knowledge, there are numerous critical problems that prevent us from commercializing the technology. One of these problems is energy loss due to the many kinds of overpotential generated in the process of mass transport in the polymer electrolyte. 2 For example, ohmic overpotential generated in the process of proton transport through this electrolyte is dependent on the water content of the electrolyte and is affected by two kinds of water transport, osmotic drag and diffusion. 3 The proton conductivity of the electrolyte decreases due to low water uptake under insufficient humidification of the supplied gases. Too much humidification causes flooding of the electrodes and consequently, the diffusion overpotential increases due to insufficient oxygen and hydrogen supply. In order to reduce these overpotentials, properties such as stable water uptake and high proton conductivity are essential for the electrolyte.An electrolyte that possesses such properties is the perfluorosulfonate ionomer membrane. Because of its chemical, mechanical, and thermal stability, as well as high proton conductivity, this ionexchange membrane is used as an electrolyte for PEFC. The constitutional formula of Nafion ͑DuPont͒, which is a typical electrolyte for PEFCs, is shown in Fig. 1. The structural characteristics of this type of membrane are hydrophobic fluorinated long main chains and short side chains bonded with hydrophilic sulfonate anion groups. Since the 1970s, various studies have been performed on this type of membrane concerning the macroscopic transport pr...