Salmonellosis in the United States is one of the most costly foodborne diseases. Given thatSalmonellacan originate from a wide variety of environments, reduction of this organism at all stages of poultry production is critical.Salmonellaspecies can encounter various environmental stress conditions which can dramatically influence their survival and colonization. Current knowledge ofSalmonellaspecies metabolism and physiology in relation to colonization is traditionally based on studies conducted primarily with tissue culture and animal infection models. Consequently, while there is some information about environmental signals that controlSalmonellagrowth and colonization, much still remains unknown. Genetic tools for comprehensive functional genomic analysis ofSalmonellaoffer new opportunities for not only achieving a better understanding ofSalmonellapathogens but also designing more effective intervention strategies. Now the function(s) of each single gene in theSalmonellagenome can be directly assessed and previously unknown genetic factors that are required forSalmonellagrowth and survival in the poultry production cycle can be elucidated. In particular, delineating the host-pathogen relationships involvingSalmonellais becoming very helpful for identifying optimal targeted gene mutagenesis strategies to generate improved vaccine strains. This represents an opportunity for development of novel vaccine approaches for limitingSalmonellaestablishment in early phases of poultry production. In this review, an overview ofSalmonellaissues in poultry, a general description of functional genomic technologies, and their specific application to poultry vaccine developments are discussed.