Hairy shaker disease (HSD) is caused by the Pestivirus border disease virus (BDV). Pestiviruses (which also include the bovine viral diarrhoea virus; BVDV) are unusual in that when they infect a pregnant female during a specified time during pregnancy, they also infect the fetus, which then becomes permanently infected with the virus. These persistently infected (PI) progeny become a constantly shedding reservoir of the virus that infects other naive animals. Currently, it is not understood how the virus evades the host immune defences. To better understand the changes to the immune system caused by this persistent infection we have looked at expression of immune related genes in PI animals and examined differences in their response to vaccinations and parasite infections. Serum and thymus tissue were collected from 3-month-old PI animals (n=8) and non-infected animals (n=10). RNA was isolated from thymus tissue and gene expression analysis was performed using Nanostring (n=6 each group). Antigen specific IgG was measured in the serum by ELISA. Decreased expression of the gene DQB was observed (p<0.05) in PI animals compared to control animals. The DQB genes are part of the MHC class II genes that are involved in the presentation of peptides to T cells. Lower antibodies to toxoplasma antigens were observed (p<0.05) in PI animals. The data is consistent with differences in the immune system of PI animals compared to controls and that the immune system in PI animals responds differently to some antigens. Understanding how the virus changes the immune system to establish a PI animal may allow development of new treatments for these viruses.