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Lymphocystis disease is one of the main viral pathologies affecting cultured gilthead seabream ( Sparus aurata ) in the Mediterranean region. Recently, we have developed a DNA vaccine based on the major capsid protein (MCP) of the Lymphocystis disease virus 3 (LCDV-Sa). The immune response triggered by either LCDV-Sa infection or vaccination have been previously studied and seem to be highly related to the modulation of the inflammatory and the IFN response. However, a comprehensive evaluation of immune-related gene expression in vaccinated fish after viral infection to identify immunogenes involved in vaccine-induced protection have not been carried out to date. The present study aimed to fulfill this objective by analyzing samples of head-kidney, spleen, intestine, and caudal fin from fish using an OpenArray ® platform containing targets related to the immune response of gilthead seabream. The results obtained showed an increase of deregulated genes in the hematopoietic organs between vaccinated and non-vaccinated fish. However, in the intestine and fin, the results showed the opposite trend. The global effect of fish vaccination was a significant decrease ( p <0.05) of viral replication in groups of fish previously vaccinated, and the expression of the following immune genes related to viral recognition ( tlr9 ), humoral and cellular response ( rag1 and cd48 ), inflammation ( csf1r , elam , il1β , and il6 ), antiviral response ( isg15 , mx1 , mx2 , mx3 ), cell-mediated cytotoxicity ( nccrp1 ), and apoptosis ( prf1 ). The exclusive modulation of the immune response provoked by the vaccination seems to control the progression of the infection in the experimentally challenged gilthead seabream., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Leiva-Rebollo, Gémez-Mata, Castro, Borrego and Labella.)