The early development of the fish immune system and its associated organs, tissues, cells and molecules can be recognized shortly after fertilization of the egg. Even though maternal effector molecules (e.g. Ig and complement) and mRNA of maternal origin encoding protective factors (complement factors, AMPs) are found in the egg stage, the developing larva has its own capacity to express immune genes shortly after fertilization. The first stem cells appear in haematopoietic intra-embryonic cell masses located in association with the developing somites and the yolk sac, and the development of thymus and kidney is noted even before the egg hatches. The development is dependent on the species and environmental parameters as differences are found between the different teleost groups due to their evolutionary background and adaptation to very different ecosystems. Various primitive myeloid and lymphoid cell types appear in the embryonic cell masses, and putative T cells colonize the thymus and putative B cells, the Bursa equivalent which is the kidney in many species. The kidney is considered the main B-cell producing organ and contains haematopoietic tissue and lymphocytes. A series of genes encoding innate and adaptive immune factors are expressed even before hatching with an accelerated development post-hatch. During the yolksac stage, the fish may prevent pathogen evasion by covering its surface with an armament of innate factors and PAMP stimulation elevates their expression. Genes encoding inflammatory cytokines such as IL-1β, IL-6, IL-8, TNF-α, iNOS, SAA, cathelicidins, and hepcidin are expressed in the yolksac larva a few hours after being exposed to pathogens. T cells and MHCII expression are localized in the thymus and IgT in the gill epithelia. The transition from a primarily innate response pattern in yolksac larvae to increased involvement of adaptive immune genes in older fry is critical as it may initially be associated with higher susceptibility to pathogen invasion. Thus, it is more difficult to infect yolksac larvae due to the strong innate and mechanical protective shield (Castro et al. Sci Rep 2015;5:15458). The development of immunocompetence, and the ability to raise a protective immune response, depends on the fish species, age, size and environmental factors, but even fry can raise a protective response following vaccination.