In recent years, experimental and theoretical methods have provided new insights into the size, shape, reactivity, and stability of clay minerals. Although diverse and complex, the surface chemistry of all clay minerals is defined spatially on a common scale of nanometres. This review is organized around the nanoscale architecture of clay minerals examined at several different length scales. The first, and perhaps most important, is the length scale associated with H bonding in clay minerals. H bonding interactions define the size and shape of 1:1 phyllosilicates and dominate the surface chemistry of many clay minerals. Structural and surface OH groups contained within and on the surface of clay minerals provide a type of `molecular reporter group' and are sensitive to subtle changes in their local environment. Examples of OH-reporter group studies in clay minerals, and the spatial scales at which they provide diagnostic information, are examined. The second length scale considered here is that associated with clay–water and clay–organic interactions. Inorganic and organic solutes can be used to explore the surface chemistry of clay minerals. Similar to the use of reporter groups, molecular probes have diagnostic properties that are sensitive to changes in their molecular environment. Clay–water interactions occur at a length scale that extends from the size of the H2O molecule (∼0.3 nm) to the larger scales associated with clay-swelling (>10 nm). Similarly, clay–organic interactions are also defined, in part, on the basis of their molecular size, in addition to the type of chemical bonding interactions that take place between the organic solute and the clay surface. Examples illustrating the use of clay–water and clay–organic solute interactions as molecular probes are presented. The largest scale to be considered is that of the particles themselves, with scales that approach micrometres. Recent developments in the synthesis and characterization of ultrathin hybrid films of clay minerals provide complementary information about the nature and distribution of active sites on clay minerals, as well as providing new opportunities to exploit the surface chemistry of clay minerals in the design of functional materials.