This study considered the range of ethical issues and potential stakeholder priorities associated with the application of genomic technologies applied to animal production systems, in particular those which utilised genomic technologies in accelerated breeding rather than the application of genetic modification. A literature review was used to inform the development of an ethical matrix, which was used to scope the potential perspectives of different agents regarding the acceptability of genomic technologies, as opposed to genetic modification (GM) techniques applied to animal production systems. There are very few studies carried out on stakeholder (including consumer) attitudes regarding the application of genomics to animal production in the human food chain and it may be that this technology is perceived as no more than an extension of traditional breeding techniques. While this is an area which needs more research, it would appear from this study that genomics, because it avoids many of the disadvantages and consumer perceptions associated with GM, is likely to prove a more publicly acceptable route than is GM for the development of healthier and more productive animals. However, stakeholders also need to have an approach to the moral status of the animals involved that finds credibility and acceptability with civil society.