Due to the minute length scales and heterogeneous nature of fuel cell components, experimental quantification of the key properties of these materials can be expensive and quite difficult to conduct, if not impossible. The objective of this work is to introduce 3-D microstructure analysis tools for "direct" quantification of the key structure-related transport measures of porous fuel cell materials. Two important microstructure analysis tools are presented for the evaluation of tortuosity and void (i.e., pore) size distribution. The first tool is aimed at quantification of the tortuosity distribution in an internal structure using a shortest path search method. The second tool is aimed at quantification of orientation-resolved chord length distributions of a phase (e.g., void, solid) in a given 3-D microstructure dataset to extract the orientation and size related statistics of a selected phase. Various other key structure metrics (e.g, phase-specific volume fraction, phase connectivity, internal surface area etc.) are also successfully extracted by using these tools. Additionally, a 3-D diffusion model is presented to determine the effective structural diffusivity coefficient based on the measured microstructure. For demonstration purposes, these methods are applied to the measured microstructure datasets of the micro-porous layer of a polymer electrolyte fuel cell. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.068203jes] All rights reserved.