The genes of the major histocompatibility complex (MHC) are prime candidates for genetic engineering of domestic species because of their importance in many biological phenomena, including disease resistance and reproduction. One MHC-linked gene, the Ped gene in the mouse, has been shown to influence embryo development and survival. The Ped gene has mapped to the Qa-2 subregion of the mouse MHC, the H-2 complex. Future studies are aimed at determining, at the DNA and protein levels, the structure of the Ped gene and its gene product. There is preliminary evidence that there may be MHC-linked Ped-like genes that influence reproduction in other species. The search for Ped-like genes in domestic species has been hampered by the limited data available describing the molecular structure of the MHC of species other than mouse and man. This paper describes the use of restriction fragment length polymorphism analysis to study the MHC of two domestic species, the pig and the chicken. Major histocompatibility complex effects on reproduction have been reported for both the pig and the chicken. The long-range goal is to identify and isolate advantageous alleles that could then be injected into recipient embryos to create more reproductively efficient animals.