Within the past few decades, intensive rearing practices have been developed to keep pace with the increasing demand for the high quality, low cost protein source that poultry provides. For example, chickens are housed routinely in crowded environments under adverse conditions and chicken strains with rapid growth, high protein-to-fat content and superior egg laying characteristics have been genetically selected. A major negative consequence of these practices has been an increase in the incidence of diseases. Enteric diseases in particular have emerged as a major problem threatening the future viability of the poultry industry. A variety of methods have been used to combat avian diseases in the commercial setting including improved farm management practices, use of antibiotic drugs, selection of disease resistant chicken strains and manipulation of the chicken immune system. In the latter category, development of vaccines against the major avian diseases has become a priority in the poultry industry. For the development of practical vaccines and new control strategies against enteric pathogens, comprehensive understanding of host intestinal immune system and basic immunobiology of host-microbes interactions leading to the protection is necessary. Recent progress in poultry genetics and functional genomics technology would facilitate the development of logical control strategies against enteric diseases of poultry in the coming decade. This paper will highlight recent progress in host immunobiology and vaccine strategies to Eimeria and Salmonella infections.