The gas diffusion layer (GDL) is one of the key components in a polymer electrolyte membrane (PEM) fuel cell. It performs several functions including the transport of reactant gases and product water to and from the catalyst layer, conduction of both electrons and heat produced in the catalyst layer, as well as mechanical support for the membrane. The overarching goal of this work is to thoroughly examine the GDL structure and properties for use in PEM fuel cells, and more specifically, to determine how to characterize the GDL experimentally ex-situ, to understand its performance in-situ, and to relate theory to performance through controlled experimentation. Thus, the impact of readily measured effective water vapor diffusivity on the performance of the GDL is investigated and shown to correlate to the wet limiting current density, as a surrogate of the oxygen diffusivity to which it is more directly related. The influence of microporous layer (MPL) design and construction on the fuel cell performance is studied and recommendations are made for optimal MPL designs for different operating conditions. A method for modifying the PTFE (Teflon) distribution within the GDL is proposed and the impact of distribution of PTFE in the GDL on fuel cell performance is studied. A method for characterizing the surface roughness of the GDL is developed and the impact of surface roughness on various ex-situ GDL properties is investigated. Finally, a detailed analysis of the physical structure and permeability of the GDL is provided and a theoretical model is proposed to predict both dry and wet gas flow within a GDL based on mercury intrusion porosimetry and porometry data. It is hoped that this work will contribute to an improved understanding of the functioning and structure of the GDL and hence advance PEM fuel cell technology.