Synapses are specialized adhesive contacts characteristic of many types of cell-cell interactions involving neurons, immune cells, epithelial cells, and even pathogens and host cells. Cell-cell adhesion is mediated by structurally diverse classes of cell-surface glycoproteins, which form homophilic or heterophilic interactions across the intercellular space. Adhesion proteins bind to a cytoplasmic network of scaffolding proteins, regulators of the actin cytoskeleton, and signal transduction pathways that control the structural and functional organization of synapses. The themes of this review are to compare the organization of synapses in different cell types and to understand how different classes of cell adhesion proteins and cytoplasmic protein networks specify the assembly of functionally distinct synapses in different cell contexts.