The high temperature environment is a concern for the coturniculture sector, since heat stress causes a reduction in weight gain, structural damage to the intestinal mucosa, immunosuppression and increased mortality. However, the thermal manipulation during incubation appears as an alternative for thermo tolerance acquisition in Japanese quail. Thus, the objective of this work was to evaluate the effects of thermal manipulation during incubation on the parameters of incubation, performance, duodenal mucosa morphometry, as well as the immune response of Japanese quails challenged thermally after hatching. Five hundred and forty eggs purchased from a commercial hatchery distributed in three commercial incubators were used, all incubators were maintained at 37,8°C, 60% humidity and automatic turning every two hours. From the 6th day of incubation until hatching temperatures were adjusted to 37,8°C (standard), 38,5°C (intermediate) and 39,5°C (high). On the 15th day of incubation the incubators were programs to stop the eggs turning. The birth of the quails was monitored every 3 hours, from the 16th to the 21th day of incubation. All unhatched eggs were opened and underwent embryodiagnosis to determine the period of embryonic mortality. The hatching quails were evaluated for physical quality from 0 to 100 points, and were weighed and evenly 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 all quails were weighed to determine live weight and weight gain. Four quails from each treatment were euthanized to collect the duodenum, cloacal pouch, liver and heart to determine absolute weight, relative weight, and to evaluate morphometry of the duodenal mucosa and the area of the bursal follicles. Four quail blood samples were collected per treatment at 30 and 40 days for hemogram, leukogram and serum biochemistry. The data were analyzed statistically and the differences between the averages were determined by the Tukey test at 5% probability. The incubation temperature 39,5°C from the 6th day of incubation reduced hatching rate and live birth weight, however, the physical quality of the quails was similar to the standard temperature. For the other variables studied, we observed a significant effect (P<0,05) of treatments on live weight, weight gain, absolute liver weight, heart, cloacal sac and in the area of the bursal follicles, where reduction occurred in these parameters when the quails were heat-challenged. At 30 and 40 days heterofilia, lymphopenia and increased heterophil/ lymphocyte ratio were observed. There was no effect (P>0,05) of incubation temperature and environment on erythrogram and proteinogram values. However, thermal manipulation during incubation at 39,5°C increased villu height, villu/crypt ratio, duodenal mucosal absorption area, and area of the bursal follicles of quails heat-challenged by heat after hatching. These results suggest that heat stress in Japanese quails reduces performance and causes immunosuppression. However, thermal manipulation during incubation can induce behavioral and physiological changes that allow the acquisition of thermotolerance in Japanese heat-challenged quail after hatching