Fish herpesviruses and their hosts may have coevolved for 400 to 450 million yr. During this coexistence, the hosts have equipped themselves with an elaborate immune system to defend themselves from invading viruses, whereas the viruses have developed strategies to evade host immunity, including the expression of cytokine genes that have been captured from the host. Taking advantage of our experimental model for cyprinid herpesvirus 3 (CyHV-3) persistence in carp, we studied the gene expression of host and virus immune-related genes in each stage of infection: acute, persistent and reactivation phases. IFNγ-1, IFNγ-2, IL-12 and IL-10 host genes, and the CyHV-3 vIL-10 gene (khvIL-10) were highly significantly up-regulated in different phases of CyHV-3 infection. Similarly, host IL-1β was up-regulated in the acute phase of CyHV-3 infection. There was no significant difference in the expression of host TNFα-1 and MHC-II genes during all phases of CyHV-3 infection. Based on the expression profile of carp immune-related genes in each stage of CyHV-3 infection, we propose a possible interaction between carp IL-12, carp IL-10 and khvIL-10 during the course of viral infection. To our knowledge, this is the first report on the expression of cytokine genes during all phases (acute, persistent and reactivation) of CyHV-3 infection.