Evidence in several species, including dogs, has been collected demonstrating that the brain hemispheres modulate the immune system in an asymmetrical way. To study the interactions between immune response and lateralization, three groups of mixed breed dogs were selected on the basis of their performance in a paw preference test involving removal of a piece of sticky tape from the snout. The expression of interleukin-2 (IL-2) and interleukin-6 (IL-6) genes was measured in left-pawed, right-pawed and ambidextrous dogs before and after immunization treatment with a rabies vaccine. The results revealed a relationship between the mRNA expression of IL-2 and IL-6 genes and the direction of behavioural lateralization. Under basal conditions, IL-2 and IL-6 gene expression was higher in left-pawed dogs than in right-pawed and ambidextrous dogs. After the vaccine administration, decreasing levels of IL-2 and IL-6 gene expression were observed in left-pawed and right-pawed dogs, but not in ambidextrous dogs. These findings represent the first evidence that brain lateralization may influence the immune system in dogs by the modulation of mRNA gene expression of cytokines such as IL-2 and IL-6, which have been recognized as key immune-regulatory proteins.