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This thesis deals with the ontogeny of select immune responses during fry stages of Atlantic cod, when exposed to two pathogens. This project addresses these areas across four experimental chapters: 1) Experimental challenges were performed to determine the effectiveness of an autologous vaccine against Vibrio anguillarum type O2! in Atlantic cod; 2) Experimental challenges were performed to determine the level of susceptibility of Atlantic cod to IPNV; 3) the characterisation of a novel protein with lysozyme activity was determined; 4) the cloning, sequencing and expression of two lysozyme genes in respect of different stimuli was assessed. Atlantic cod fry of 4 different size groups were used to test the effectiveness of the autologous vaccine against O2! Vibrio anguillarum. This developmental size range demonstrated a switch from the innate immune system to favour the adaptive immune system occurring when Atlantic cod reach 1.5g in size. Atlantic cod of 1, 3 and 10g in size were selected to determine susceptibility of IPNV. Viral titre analysis and immunohistochemistry for the IPN virus was used to confirm viral location and replication within the fish. At 1g in size Atlantic cod are susceptible to IPNV; the virus is able to replicate within the fish to a level causing mortality. At 3g in size IPNV are able to infect the fish but viral replication does not occur to the same level as that observed with 1g fish and observations of mortality were reduced. At 10g, Atlantic cod are asymptomatic carriers of the virus. The characterisation of a novel protein with lysozyme activity was determined using purification techniques, and functional assays. The isolation and sequencing of the Atlantic cod lysozyme gene revealed two different isoforms of the gene. Expression studies demonstrated that components of bacterial makeup increased the expression of lysozyme gene compared to the relative control. Using immunostimulants LPS and PHA in larger fish (200g) a down regulation of both lysozyme genes was observed relative to their corresponding controls.