Aquaculture still faces serious economic impacts due to the loss of animals to disease. A conservative estimate of 5% losses due to disease means that the finfish aquaculture industry loses over $1 billion annually on a global scale. One proven way to prevent costly disease outbreaks is to vaccinate fish against common or known pathogens. Current vaccination schemes still result in losses, however, and this may be due in part to vaccine design. Vaccines are currently designed using state of the art knowledge of immune responses, which is based primarily on mammalian studies. Just how applicable is this information to fish immunity and vaccine design, however? This review discusses what is currently known for teleost fish about two key processes that drive immune response: antigen presentation and cytokine regulation. In both cases many of the genes known to be involved have been identified; in the case of cytokines recent genome projects have added to the total rapidly in recent years. Most functional studies to date in these areas have focused on gene expression and mRNA levels, due to a lack of available antibodies that are required for studies at the protein level. These studies are confounded by the fact that in many cases the teleost equivalents of single copy mammalian genes are duplicated and are regulated in very different ways. This suggests that vaccines designed around mammalian immunological principles will not be as efficient as they could be. Future research goals for fish immunologists should be to develop the antibodies required for protein level functional studies in order to provide the true understanding of fish immunity that is required for the design of finfish aquaculture vaccines that are truly effective.