Neuropeptides support inter-cell communication and have a role in many diverse biological processes. For pig, a biomedical model, few prohormones from which neuropeptides result after convertase processing are listed in the UniProt database. Therefore, our goals are to obtain an in silico library of pig prohormone and convertase genes and to functionally annotate these genes based on a large number of complementary gene expression microarray experiments. Using a bioinformatics pipeline, 101 prohormone genes and 8 convertase genes known in human, rat, mouse, chicken, and cow were located in the pig genome. Frequently (P-value < 0.005) differentially expressed prohormone genes included adrenomedullin (ADML), augurin (AUGN), neuropeptide Y (NPY), proenkephalin-A (PENK), parathyroid hormone-related protein (PTHR), and vascular endothelial growth factor C (VEGFC) and convertases (PCSK1 and PCSK7). Embryo and placental tissues displayed the most differentially expressed genes. Our genomic characterization allows the use of the pig as an effective animal model to gain a deeper understanding of neuropeptides.