Addition of pituitary adenylate cyclase-activating polypeptide (PACAP) into the cultured PC12 cells secreted dopamine and promoted neurite outgrowth of the cells, indicating cell differentiation. To characterize the PACAP-differentiated PC12 cell transcriptome, we applied DNA macroarray techniques, using Atlas Rat 1.2 Array membranes (BD Biosciences Clontech) that have 1176 cDNA. RNA samples were harvested from PC12 cells before and at a time of 6 h treatment with 1 nM PACAP, when neuritogenesis was remarkably observed under the condition used. Several genes regulated by PACAP have been associated with neuritogenesis (i.e. villin 2 and tissue plasminogen activator) or cell growth/differentiation (i.e. cyclin or ornitine decarboxylase). Also, cytoskeleton proteins such as actin or tubulin were up-regulated for cell morphology remodeling. A message of vehicle trafficking molecule (synaptotagmin IV) was more remarkably increased (3.95-6.85-fold). Signaling molecules such as small G proteins (rab12, rab16, or ral), IkappaB, or STAT3 were altered by PACAP. It is noteworthy that PACAP inhibited the expression of galanin receptor 2, whose ligand was shown to inhibit tyrosine hydroxylase activity. Thus, in this study the transcriptome of PACAP-differentiated PC12 was established, leading to the elucidation of the molecular mechanism of neuritogenesis by the neuropeptide.