Chronic prolactin (PRL) exposure can affect several functions of duodenal epithelia, especially those associated with fluid and electrolyte transport. However, little is known regarding its molecular mechanism. To identify PRL-regulated genes, microarray analysis was performed on RNA samples from duodenal epithelial cells of anterior pituitary (AP)-grafted hyperprolactinemic rats. Herein, we identified 321 transcripts upregulated and 241 transcripts downregulated after 4 weeks of AP transplantation. Results from real-time PCR analyses of 15 selected genes were consistent with the microarray results. Gene ontology analysis demonstrated pleiotropic effects of PRL on several cellular processes, including cellular metabolic process, cell communication and cell adhesion. Interestingly, 17 upregulated transcripts and 12 downregulated transcripts are involved in the transport of ions and nutrients, e.g., Ca(2+), Na(+), K(+), Cl(-) and glucose, thus agreeing with the established action of PRL on electrolyte homeostasis. The present results provided fundamental information for further investigations on mechanism of PRL actions in the intestine.