Porous metal-organic frameworks (MOFs) are the subject of considerable research interest because of their high porosity and capability of specific binding to small molecules, thus underpinning a wide range of materials functions such as gas adsorption, separation, drug delivery, catalysis, and sensing. MOFs, constructed by the designed assembly of metal ions and functional organic linkers, are an emerging class of porous materials with extended porous structures containing periodic binding sites. MOFs thus provide a new platform for the study of the chemistry and reactivity of small molecules in confined pores using advanced diffraction and spectroscopic techniques. In this review, we focus on recent progress in experimental investigations on the crystallographic, dynamic and kinetic aspects of substrate binding within porous MOFs. In particular, we focus on studies on host-guest interactions involving open metal sites or pendant functional groups in the pore as the primary binding sites for guest molecules.