Koi herpesvirus (KHV), viral pathogen of common carp, causes severe losses in common carp production all over the world. The KHV genome contains a carp IL-10 homologue gene and two types of secreted TNF receptor family (TNFRF) genes. Cytomegalovirus IL-10 homologue is known to attenuate host innate immune responses. Poxvirus TNFRFs have roles in immune evasion in the host. Therefore, KHV may perturb host immune responses by secreting these molecules. In this study, carp gills transcriptome during KHV infection was analyzed using oligo-DNA microarray to elucidate the immuno-suppressive effect of KHV in the host. Gills of infected common carp with KHV were sampled before challenge and at 3, 7 and 9 days post-infection. Total RNA were extracted from the gills and then Cy3 labeled cRNA were synthesized. The cRNA were hybridized with DNA oligo microarray containing 10,823 unique genes of common carp and 152 unique genes of KHV. 786 genes of common carp significantly showed more than 2-fold change than control. Of the 30 immune related genes differently regulated, 15 genes up-regulated during KHV infection included Mx protein, the genes started to up-regulate at 7 days after challenge. In contrast, 15 genes down-regulated during KHV infection included immunoglobulin light chain and MHC class II beta chain, the genes started to down-regulate at 3 or 7 days after challenge. On the other hand, 20 genes of KHV were markedly detected at 7 days after challenge.