The gastro-intestinal tract serves as the route of infection of most bacterial pathogens in fish, and the immune response genes in the gut produce substances that provide an initial defense during pathogen invasion. The expression of some genes involved in antibacterial defense, cell-mediated immunity and inflammation in the distal intestine of Atlantic cod, Gadus morhua L., was investigated following intraperitoneal vaccination with heat-killed Vibrio anguillarum. Tissue samples of the distal intestine were collected at 0, 1, 3, 7 and 10 days post-vaccination (dpv) and processed for semi-quantitative RT-PCR analyses. Expression of the bactericidal/permeability-increasing protein/lipopolysaccharide-binding protein (BPI/LBP), g-type lysozyme, non-specific cytotoxic cell receptor protein-1 (NCCRP-1) and interleukin-8 (IL-8) significantly increased during the early stages post-vaccination, that is, 1-3 dpv, followed by a decrease in their expression returning to their initial levels. Transferrin and apolipoprotein A-I, although weakly expressed in the distal intestine, also increased in the vaccinated fish. Interleukin-1 beta (IL-1 beta) was significantly decreased in its expression level relative to the PBS-injected fish at 3 and 7 dpv. The expression of these immune-related genes in the distal intestine as a result of vaccination provides valuable information on the mechanisms of gut immunity in the fish against pathogenic bacteria, particularly during the early stages of infection.