Because of the fine grain size in most as-deposited polycrystalline films, grain boundaries control the observed mass transport, at least at temperatures less than one-half of the absolute melting temperature. Thus, a study of the effect of structure on grain boundary diffusion is one objective of this chapter. However, mass transport also occurs in monocrystalline films where the point defect structure controls the rate of transport through the lattice. Surface diffusion is also of interest primarily in deposition processes, but also in applications as well. We will examine the effect of structure on all three modes of transport. Further, we will discuss examples where these various types of transport affect properties. Some thin films are amorphous and mass transport in some of them has practical import. Consequently, we will devote some discussion to this topic. Diffusion barriers are used to prevent diffusion between layers. Hence, we will examine what aspects of structure affect the ability of diffusion barrier materials to prevent such atom transport and to prevent chemical reactions with the adjacent layers. The effect of pre-existing structure on the course of reactions between layers will also be considered. Finally, the effect of defects introduced via radiation on the rates of reactions will be discussed.