The poultry gut harbours a diverse microbiota, which plays a pivotal role in host nutrient utilization and health. Although the majority of this microbiota is commensal bacteria, pathogens are also present. Commensal and pathogenic microbes interact with each other, either positively or negatively, profoundly affecting host nutrition and incidence of infection. A better understanding of the gut pathogen-microbiota interaction is essential to address the current challenges in poultry production. Recent studies using metagenomics have helped gain new insights into the interactions between the gut pathogens and commensal microbes in poultry. This chapter reviews the current understanding and discusses the knowledge gaps surrounding the interaction between gut microbiota and pathogens in poultry, and also future research needs. The intestinal pathogens discussed in this chapter include Escherichia, Salmonella, Clostridium, Campylobacter, Eimeria and viruses. Starting with an introduction to these pathogens and their associated diseases, there then follows a section on the interactions between these pathogens and microbiota, and their impact on host nutrition and health.