Synaptic dysfunction is a key process in the evolution of many neurodegenerative diseases, with synaptic loss preceding that of neuronal cell bodies. In Alzheimer, Huntington, and prion diseases early synaptic changes correlate with cognitive and motor decline, and altered synaptic function may also underlie deficits in a number of psychiatric and neurodevelopmental conditions. The formation, remodelling and elimination of spines and synapses are continual physiological processes, moulding cortical architecture, underpinning the abilities to learn and remember. In disease, however, particularly in protein misfolding neurodegenerative disorders, lost synapses are not replaced and this loss is followed by neuronal death. These two processes are separately regulated, with mechanistic, spatial and temporal segregation of the death 'routines' of synapses and cell bodies. Recent insights into the reversibility of synaptic dysfunction in a mouse model of prion disease at neurophysiological, behavioral and morphological levels call for a deeper analysis of the mechanisms underlying neurotoxicity at the synapse, and have important implications for therapy of prion and other neurodegenerative disorders.