Research has shown that gut microbiota; the bacteria, archaea, protozoa, fungi and viruses that reside within the gastrointestinal tract, has a profound effect on the health and productivity of poultry. This chapter outlines what is known about the establishment and development of the gut microbiota, some of the mechanisms by which the microbiota can affect poultry and the ways that the microbiota can be manipulated to enhance poultry health and productivity. Firstly, an overview of the microbiota of chickens is presented. This is followed by a discussion on the functional interaction of such microbiota with the host, in this case, the chicken. A section on the manipulation of microbiota for health and productivity of chickens is provided, covering the use of microbes to manipulate gut microbiota and also the use of feed additives and antibiotics. The chapter concludes with an overview of future trends in research.