Agrin is a motoneuron-derived signaling factor that plays a key organizing role in the initial stages of neuromuscular synapse formation. Agrin is expressed in other regions of the developing central and peripheral nervous systems, however, raising the possibility that it also directs the formation of some interneuronal synapses. To address this question, we have examined the expression and localization of agrin during formation of cholinergic, interneuronal synapses in the sympathetic system. In the superior cervical ganglia (SCG) in vivo, we found that agrin is highly expressed, and that it is present at, but is not limited to, synapses. In SCG neuronal cultures that were treated with ciliary neurotrophic factor to induce a uniform cholinergic phenotype, we found that agrin immunostaining colocalized precisely with cholinergic terminals and aggregates of neuronal acetylcholine receptor on the neuronal cell bodies and dendrites. Moreover, we found that alpha-dystroglycan, which is a potential receptor for agrin, is also concentrated at these cholinergic synaptic contacts. Finally, the SCG neurons expressed the C-terminal isoform of agrin that is neural-specific and highly active in synaptogenesis, and also the N-terminal splice isoform that occurs as a type II transmembrane protein. These findings show that agrin is specifically localized at sympathetic synapses in vitro, and are consistent with it playing a role in interneuronal synapse formation.