The high and preferential expression of the PAC(1)(short)HOP1 receptor in postganglionic sympathetic neurons facilitates microarray studies for mechanisms underlying PACAP-mediate neurotrophic signaling in a physiological context. Replicate primary sympathetic neuronal cultures were treated with 100 nM PACAP27 either acutely (9 h) or chronically (96 h) before RNA extraction and preparation for Affymetrix microarray analysis. Compared to untreated control cultures, acute PACAP treatment modulated significantly the expression of 147 transcripts of diverse functional groups, including peptides, growth factors/cytokines, transcriptional factors, receptors/signaling effectors and cell cycle regulators, that collectively appeared to facilitate neuronal plasticity, differentiation and/or regeneration processes. Some regulated transcripts, for example, were related to BDNF/TrkB, IL-6/Jak2/Socs2 and TGF/follistatin signaling; many transcripts affected bioactive peptide and polyamine biosynthesis. Although chronic PACAP treatments altered the expression of 109 sympathetic transcripts, only 43 transcripts were shared between the acute and chronic treatment data sets. The PACAP-mediated changes in transcript expression were corroborated independently by quantitative PCR measurement. The PACAP-regulated transcripts in sympathetic neurons did not bear strong resemblance to those in PACAP-treated pheochromocytoma cells. However, many PACAP-targeted sympathetic transcripts, especially those related to peptide plasticity and nerve regeneration processes, coincided significantly with genes altered after peripheral nerve injury. The ability for sympathetic PAC(1)(short)HOP1 receptors to engage multiple downstream signaling cascades appeared to be reflected in the number and diversity of genes targeted in a multifaceted strategy for comprehensive neurotrophic responses.