The diverse intestinal microbiota of poultry plays critical roles in determining feed utilization, health, and diseases. A comprehensive understanding of how various factors shape the intestinal microbiota in poultry can help develop new dietary and managerial interventions to enhance bird growth, maximize feed utilization efficiency, and lower enteric diseases caused by pathogens. This chapter reviews the current understanding of how different factors (except diet and growth promoters that are covered in other chapters of this book) can affect the intestinal microbiota. These factors include genetics and breeds, hatchery conditions and environment, bedding and litter, climate and geographic regions, gender and diseases. Finally, the chapter looks ahead to future perspectives in research on intestinal microbiota in poultry and provides comprehensive guidance on finding further information on this area.