The aim of this study was to evaluate the effects of glutamine and threonine supplementation on the ileal mucosa of broilers aged 21-42 days. Six-hundred and forty-one-day old chicks of the Cobb Slow lineage were utilized in this study. From 1 to 21 days of age, the chicks received a commercial diet; and after 22 days, the broilers were distributed in a completely randomized design in a 2 ? 4 factorial scheme (challenge and diet), with 4 replications and 20 chicks per experimental unit. At 22 days of age, the challenged broilers received a commercial vaccine against coccidiosis. A commercial diet was utilized as control and three other diets were formulated with reduced crude protein (-3%), and were corrected with the addition of glutamine (Gln) and glutamic acid (Glu) as non-specific nitrogen sources, and finally supplemented with L-Threonine (Thr) at 0.70, 0.80, and 0.85% digestible threonine, respectively. At 28 days of age, diets with Gln/Glu + Thr resulted in greater ileal villi lengths. Challenge with Eimeria sp. reduced the number of goblet cells and increased the duodenal and jejunal crypt depths. At 42 days of age, an interaction was observed between diet and challenge in relation to ileal villi length; better results were observed in the challenged broilers that received 0.85% Gln/Glu + Thr. The mucosal morphology in the ileal villi extremities was preserved in the challenged broilers that received higher Thr levels in their diets. The results suggested that the inclusion of glutamine and threonine affected the morphometry and mucosa of the ileum, thereby improving the mucosal quality.