Since Donald J. Cram's first synthesis of a carcerand, which permanently entrapped a single guest molecule, many other carcerands and hemicarcerands have been synthesized and studied. Slowly, we begin to understand the role of the template in the formation of hemicarceplexes and carceplexes, why some hemicarceplexes are more stable than others, and how guests enter and exit the inner phases of molecular containers. In this Account we discuss our new insight in the chemistry of molecular containers, as well as recent highlights in through-shell chemistry and in the inner-phase stabilization of reactive intermediates.