Neurons in the brain form complex neural circuits by connecting to each other through highly specialized junctions called synapses. A molecular logic underlies the formation, establishment and properties of each of these synapses and is likely driven by synaptic cell adhesion molecules. We aim to understand the protein complexes formed at these junctions and how they assemble and arrange in respect to each other in the synaptic cleft with the overall aim to understand the extracellular architecture of the synapse. We use a combination of cryo-electron microscopy, electron cryo-tomography and biophysical techniques to understand their interactions at a molecular level and relate concepts determined in vitro back to biology. Our approach identifies the building blocks of the synapse and will help to understand how these crucial elements of our nervous system are assembled.