Mutations in many genes encoding proteins involved in various aspects of synapse formation and function have been implicated in specific neurodevelopmental syndromes. More recent findings show that this class of genes more generally represents a major mutational target for common neurodevelopmental and neuropsychiatric disorders, including intellectual disability, autism, schizophrenia and epilepsy. Synaptic genes have thus become a focus of research on neurodevelopmental disorders, contributing to our understanding of disease pathogenesis and providing promising therapeutic targets. Here, we consider the molecular processes of synapse formation and plasticity and how mutations in many genes with distinct functions in these processes lead to neurodevelopmental disorders.