A number of receptor-mediated events are thought to control the structural changes occurring at synapses which underly neural plasticity. There is growing evidence that these include the actions of serine proteases which, through the protease-activated receptor (PAR) family, cause remodelling of presynaptic terminals. A balance between structural fluidity and stability is achieved through the immobilization by covalent cross- linking of structural glycoproteins, cytokines and protease inhibitors in the synaptic region by transglutaminases. This article considers the existing evidence of role for transglutaminase in synaptic competition during neuromuscular development and in cerebellar granule cell development. We propose a hypothesis for the interaction between protease and transglutaminase activity in contact stabilization.