Food-borne pathogenic bacteria are all too often found as commensal or transient organisms in the gastrointestinal tract of poultry. Many of these organisms do not reveal themselves through illness in the bird, although some do. Therefore, it is important to find ways to apply treatment to all members of a flock, rather than simply treating ‘sick’ birds. This chapter describes the gastrointestinal microbiota of poultry before going on to consider alternatives to the use of antibiotics. The chapter considers the use of organic acids, bacteriophages, sodium chlorate and pro- and prebiotic approaches.