Agrin is a synapse-organizing protein likely to mediate nerve-induced aggregation of acetylcholine receptors and other postsynaptic components at the neuromuscular junction. We used in situ hybridization and polymerase chain reaction (PCR) to define the localization of agrin mRNA and its alternatively spliced forms in the chick embryo nervous system. Agrin cRNA probes intensely labeled motor neurons, dorsal root ganglia, cerebellar Purkinje neurons, and retinal ganglion cells. Neuronal layers in optic tectum and ventricular regions were also labeled. Analysis by PCR showed that all parts of the nervous system at embryonic day 10 contained three major forms of agrin mRNA. Our results raise the possibility that agrin isoforms play a role in synapse formation or other aspects of neuronal development in the central nervous system.