ABSTRACT This study aimed to evaluate the effects of different temperatures on incubation variables, performance, and morphometry of the duodenal mucosa of Japanese quails (Coturnix coturnix japonica) submitted to chronic heat stress after hatching. We distributed 540 eggs in three incubators with a temperature of 37.8°C and 60% of humidity. From the 6th day of incubation until hatching, the temperatures were adjusted to (37.8°C, 38.5°C and 39.5°C). After hatching, quails were evaluated for the quality score, weighed, and distributed in a completely randomized design with three incubation temperatures (37.8, 38.5, and 39.5°C) and two ambient temperatures (stress and thermoneutral). At 10, 20, 30, and 40 days they were weighed to determine the live weight (g) and weight gain(g). To collect the duodenum and determine morphometric parameters, we euthanized four quails of each treatment. The data were analyzed, and the differences between the means determined by the Tukey test at 5%. The incubation temperature of 39.5°C provided lower hatching rate and the live weight at birth; however, from the 10th day of age, increased live weight, weight gain, and positively influenced the morphological parameters of the duodenal mucosa in situations of chronic stress.