Development of pre- and postsynaptic specializations at the vertebrate neuromuscular junction is affected by molecules concentrated in the extracellular matrix of the synaptic cleft. Agrin, laminin beta 2 and ARIA are the best characterized proteins known to be involved in particular aspects of synaptic differentiation. Recent advances in defining the domains of these molecules that are crucial for their synapse-organizing activity and their localization to synaptic basal lamina will help our understanding of the molecular mechanisms involved in synapse formation.