Significant advances have been made in recent years in improving animal stocks by selective breeding. However, existing selection techniques still rely on laborious and time-consuming progeny-testing programs and often depend on subjective assessment of the phenotype. New techniques in molecular genetics are being developed, aimed at the isolation and identification of DNA markers linked to genes for economically important production traits and disease resistance. When available, these markers will provide animal breeders with an objective test system to identify, at birth or even earlier, animals carrying desirable genes. This review outlines some of these new techniques and how they may be applied to the animal industries. Consideration is also given to some of the recent advances in our understanding of the immune system and of possible mechanisms of genetic control of animal disease resistance or susceptibility. The current knowledge of major histocompatibility complex (MHC) and non-MHC associated disease resistance/susceptibility in domestic animals is summarised and mechanisms which may be responsible for these associations are presented. Genes that control such factors as macrophage activation, cytokines, cytokine receptors and gamma delta-T cell receptors are also presented as potential candidates for analysis in genetic disease association studies. Ultimately, the goal will be to identify genes or DNA markers which can be used to select for or to genetically engineer disease resistance and enhanced production traits.