The allocation of energetic resources into competing physiological systems is crucial for the survival and fitness of an organism. Maintenance of active growth and effective immune function is energetically costly and therefore, trade-offs should have evolved to optimise the allocation of resources into these systems according to physiological status. While recent studies have begun to elucidate the mechanisms by which cross-talk exists between these two systems, more work is needed to characterise their interactions. A high-throughput proteomics approach was developed to investigate the molecular mechanisms underpinning fast growth and molecular cross-talk between growth and immune function. This approach revealed unique routes to fast growth in two different growth-accelerated coho salmon strains, including increased protein synthesis in fish overexpressing growth hormone (GH) through a focussed up-regulation of translation machinery. Conversely, selectively-bred fish showed more complex alterations in multiple metabolic pathways potentially underlying increased growth and domestication. Additionally, the liver proteome response of rainbow trout to a bacterial challenge unveiled host defence and immune proteins upregulated during the acute phase response (APR), along with candidate proteins involved in re-allocation of energetic resources during an immune response. Additionally, novel genetic expansions of salmonid complement C3 proteins upregulated during bacterial challenge were identified and characterised. Finally, the AMP-activated kinase (AMPK) system was investigated due to its role in managing energetic status, making it an ideal system to investigate crosstalk between growth and immunity. Novel salmonid-specific genetic expansions in AMPK subunits (α, β and γ) were demonstrated and their mRNA level expression analysed in fast-growing fish strains exposed to immune stimuli, where an increase in expression of several subunits was observed for fish overexpressing GH. However, a significant downregulation in expression of several AMPK subunit genes occurred in response to immune stimuli. Overall, this project provides insights into links between growth and immune function in salmonids, which are relevant to the aquaculture industry, where the aim is to maximise fish growth while retaining strong immunocompetence.