In recent years, because of the shortage of human organ donors, xenotransplantation has become an emergency alternative option. Because pigs are the major donors for xenotransplantation, a variety of porcine viruses have become a threat to the human recipients. Porcine endogenous retroviruses and porcine lymphotropic herpesvirus 1 and 2 have previously been identified as major concerns for organ transplantation; however, the ubiquitous nature of herpesviruses, including PCMV, means that these viruses are now a major focus in the development of xenotransplantation technology. PCMV inhibits host immune function and defense mechanisms, particularly the action of T lymphocytes. Like porcine reproductive and respiratory syndrome virus, PCMV uses alveolar macrophages as target cells, and a recent study showed that PCMV infection can promote the occurrence of porcine reproductive and respiratory disease. Microarray technology is used to monitor target molecules by detecting the intensity of hybridization signals, and it is capable of both high-throughput and high sensitivity. It can detect transcriptional level changes in entire host genomes in response to pathogens, allowing a more detailed understanding of the molecular mechanisms of host-pathogen interactions during viral infection. Although a series of transcriptome profiles have been generated for the host in response to herpesvirus family infections, a specific transcriptome analysis of the host following PCMV infection that focuses on the immunosuppressive molecular mechanisms of PCMV is still lacking. The current research used the Agilent Pig 4644K Gene Expression Microarray v2 to comprehensively analyze differences in the transcriptomes of the thymuses of pigs infected with PCMV compared with those of control pigs. The expression of a group of immune-related genes identified by the microarrays was confirmed by quantitative RT-PCR and western blot. The results of this study further both our understanding of the genes involved in the porcine immune response to PCMV and the pathogenesis of PCMV, and they will contribute to the prevention and LDN-193189 treatment of immunosuppressive viral diseases. The interaction between a virus and its host is determined by the host’s immune response. Like human cytomegalovirus, PCMV suppresses the immune system, especially the cell-mediated immune response ; however, there has been no research into the immune-evasion mechanism of PCMV until now. The thymus is one of the most important central immune organs, which is mainly composed of lymphocytes, macrophages, dendritic cells, epithelial cells, and reticular cells. The thymus is the main site of the proliferation, differentiation, and maturation of immune cells. It plays a crucial regulatory role in the development and immune function of peripheral immune organs. Changes in the thymus transcriptome during infection with an immunosuppressive virus directly reflect the impact of the virus on the immune function of host, which is the reason we chose the thymus as the site for our microarray experiments.