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Even though the intestine represents a small proportion of body weight in broiler chickens, its requirements for energy and nutrients are high. A healthy broiler intestine has a well-coordinated immune system that must accommodate commensal microbiota while inhibiting the colonization and proliferation of harmful pathogens. Modern commercial intensive practices impose a high sanitary pressure that may exacerbate the progression of intestinal diseases such as coccidiosis and necrotic enteritis. The incidence of these diseases may increase worldwide due to mounting pressure to limit the use of subtherapeutic antibiotics as growth promoters or ionophores for coccidial suppression/prevention in the diets of broilers. For this reason, altering dietary concentrations of some amino acids, particularly trophic amino acids, may be beneficial to modulate the intestinal physiology, immunology, and microbiology of broilers. Trophic amino acids, such as threonine, arginine, and glutamine, play a very important role on the intestinal mucosa and may support increased epithelial turnover rates to improve intestinal recovery following an insult. Furthermore, these amino acids may help to minimize over-activation of the innate immune system, which is the most expensive in terms of nutrients and energy, as well as modulate the intestinal microbiota. The objective of this review is to provide insight into the potential role of trophic amino acids in these processes and report some updated studies of their use in diets for broiler chickens.