Prolactinomas are the most common secretory pituitary tumors; however, their pathogenesis is unclear. In order to explore the pathogenesis of prolactinomas, we used fiber-optic BeadArray to examine gene expression profiles in five prolactinomas compared with three normal pituitaries. Three down-regulated genes and one up-regulated gene were chosen for validation by quantitative real-time reverse-transcription polymerase chain reaction. We then performed pathway analysis on the identified differentially expressed genes using the Kyoto Encyclopedia of Genes and Genomes. Array analysis showed significant increases in the expression of 27 genes and 3 expressed sequence tags (ESTs), and decreases in 182 genes and 9 ESTs, including HIG1 domain family, member 1B, S100 calcium binding protein A9, angiopoietin 2, interleukin 8, hydroxyprostaglandin dehydrogenase 15-(NAD), suppression of tumorigenicity18, and WNT inhibitory factor 1. Pathway analysis showed that the P53 and GnRH signaling pathways may play an important role in tumorigenesis of prolactinomas. Our data suggest fiber-optic BeadArray combined with pathway analysis of differential gene expression profile appears to be a valid approach for investigating the pathogenesis of tumors.