The extracellular matrix is an insoluble aggregate of large proteins and glycosoaminoglycans that comprises the microenvironment of cells in tissue. The matrix displays a host of ligands that interact with cell-surface receptors to mediate the attachment and spreading of cells and regulate signaling processes. Studies of cell-matrix interactions and downstream signaling processes commonly employ substrates having an adsorbed layer of protein and are challenged by the difficulty in controlling the structure and activity of the immobilized protein. Significant effort has been directed towards the development of model substrates that present adhesion ligands in defined densities, orientations and environments. Among these approaches, self-assembled monolayers of alkanethiolates on gold offer a high level of control over the molecular structure of the surface and are well-suited to studies of cell adhesion. This review describes the design and use of monolayers for applications in cell biology, including the use of monolayers to evaluate the roles of peptide and protein ligands in cell-matrix interactions, the development of methods to pattern ligands on monolayers and applications to cell biology, the development of dynamic monolayers that can switch the activities of ligands presented to an adherent cell, and the rewiring of interactions between a cell and its substrate. These examples illustrate the flexibility inherent to monolayers for applications in cell biology.