Intercalation compounds, used as electrodes in Li-ion batteries, are a fascinating class of materials that exhibit a wide variety of electronic, crystallographic, thermodynamic, and kinetic properties. With open structures that allow for the easy insertion and removal of Li ions, the properties of these materials strongly depend on the interplay of the host chemistry and crystal structure, the Li concentration, and electrode particle morphology. The large variations in Li concentration within electrodes during each charge and discharge cycle of a Li battery are often accompanied by phase transformations. These transformations include order-disorder transitions, two-phase reactions that require the passage of an interface through the electrode particles, and structural phase transitions, in which the host undergoes a crystallographic change. Although the chemistry of an electrode material determines the voltage range in which it is electrochemically active, the crystal structure of the compound often plays a crucial role in determining the shape of the voltage profile as a function of Li concentration. While the relationship between the voltage profile and crystal structure of transition metal oxide and sulfide intercalation compounds is well characterized, far less is known about the kinetic behavior of these materials. For example, because these processes are especially difficult to isolate experimentally, solid-state Li diffusion, phase transformation mechanisms, and interface reactions remain poorly understood. In this respect, first-principles statistical mechanical approaches can elucidate the effect of chemistry and crystal structure on kinetic properties. In this Account, we review the key factors that govern Li diffusion in intercalation compounds and illustrate how the complexity of Li diffusion mechanisms correlates with the crystal structure of the compound. A variety of important diffusion mechanisms and associated migration barriers are sensitive to the overall Li concentration, resulting in diffusion coefficients that can vary by several orders of magnitude with changes in the lithium content. Vacancy clusters, groupings of vacancies within the crystal lattice, provide a common mechanism that mediates Li diffusion in important intercalation compounds. This mechanism emerges from specific crystallographic features of the host and results in a strong decrease of the Li diffusion coefficient as Li is added to an already Li rich host. Other crystallographic and electronic factors, such as the proximity of transition metal ions to activated states of hops and the occurrence of electronically induced distortions, can result in a strong dependence of the Li mobility on the overall Li concentration. The insights obtained from fundamental studies of ionic diffusion in electrode materials will be instrumental for physical chemists, chemical engineers, synthetic chemists, and materials and device designers who are developing these technologies.