Since their first synthesis in the 1940s, zeolites have found wide applications in catalysis, ion-exchange, and adsorption. Although the uniform, molecular-size pores of zeolites and their excellent thermal and chemical stability suggest that zeolites could be an ideal membrane material, continuous polycrystalline zeolite layers for separations were first prepared in the 1990s. Initial attempts to grow continuous zeolite layers on porous supports by in situ hydrothermal synthesis have resulted in membranes with the potential to separate molecules based on differences in molecular size and adsorption strength. Since then, further synthesis efforts have led to the preparation of many types of zeolite membranes and better quality membranes. However, the microstructure features of these membranes, such as defect size, number, and distribution as well as structure flexibility were poorly understood, and the fundamental mechanisms of permeation (adsorption and diffusion), especially for mixtures, were not clear. These gaps in understanding have hindered the design and control of separation processes using zeolite membranes. In this Account, we describe our efforts to characterize microstructures of zeolite membranes and to understand the fundamental adsorption and diffusion behavior of permeating solutes. This Account will focus on the MFI membranes which have been the most widely used but will also present results on other types of zeolite membranes. Using permeation, x-ray diffraction, and optical measurements, we found that the zeolite membrane structures are flexible. The size of defects changed due to adsorption and with variations in temperature. These changes in defect sizes can significantly affect the permeation properties of the membranes. We designed methods to measure mixture adsorption in zeolite crystals from the liquid phase, pure component adsorption in zeolite membranes, and diffusion through zeolite membranes. We hope that better understanding can lead to improved zeolite membranes and eventually facilitate the large-scale application of zeolite membranes to industrial separations.