Agrin is an extracellular matrix protein that has been implicated as a synaptogenic agent in the peripheral and central nervous systems. Both the level of expression and pattern of alternative splicing of agrin mRNA are developmentally regulated. As a step toward identifying signals important in regulating agrin gene expression in neurons, we examined the effects of postganglionic axotomy or preganglionic denervation on agrin mRNA levels and alternative splicing in ciliary ganglia of posthatch chicks. In comparison to unoperated age-matched controls, in situ hybridization with a pan-specific agrin cRNA probe demonstrated a significant decrease in neuronal agrin mRNA expression as a result of axotomy. Reverse transcription-polymerase chain reaction analysis demonstrated that axotomy also resulted in changes in the pattern of alternative splicing of agrin mRNA. Underlying these changes are decreases in the molar amounts of transcripts encoding the neuron-specific isoforms agrin8 and agrin19, homologous to rat agrin proteins that have high AChR aggregating activity. Similar, but less dramatic changes in agrin expression following axotomy were also observed in unoperated neurons on the contralateral side. In contrast, the only significant change in agrin gene expression following ganglionic denervation was a small decline in the relative abundance of agrin 8 mRNA in operated versus unoperated age-matched control ganglia. Major changes in agrin gene expression following axotomy but not denervation are consistant with the notion that agrin synthesized by ganglionic neurons exerts its effects in the periphery rather than at synapses formed between ciliary ganglion neurons and their preganglionic input. These data suggest that the pattern of alternative splicing and the absolute amount of agrin mRNA in ciliary ganglion neurons may be regulated by target tissue interactions.