Synaptic transmission is fundamental for our sensory, motor and cognitive capabilities. Like many other cellular processes, it requires a precise coordination of molecular pathways that are carried out by multiple macromolecular complexes organized in functional units. While physiological experiments, interaction data, and structural studies of purified systems were essential for our understanding of the function of the individual complexes involved, they cannot combine high structural detail with the unperturbed organization of complexes within cells to resolve how the actions of individual complexes integrate. Cryo-electron tomography (cryo-ET) allows us to simultaneously image multiple protein complexes and lipids at a single nanometer resolution in their native composition, conformation and environment. Our goal is to determine morphological properties, precise localization and molecular identity of complexes at mammalian synapses, and to elucidate the molecular architecture of large trans-synaptic molecular assemblies. These would complement data obtained from methods, and allow us to precisely determine the function of synaptic complexes and obtain a comprehensive picture of synaptic transmission, plasticity and synaptopathies.