Pigs exposed to heat stress (HS) increase body temperature in which can damage the intestinal epithelia and affect the absorption and availability of AA. Protein digestion and metabolism further increase body temperature. An experiment was conducted with 6 pairs of pigs (of 47.3 ± 1.3 kg initial BW) exposed to natural HS to assess the effect of substituting dietary protein-bound AA by free AA on morphology and gene expression of intestinal epithelial, and serum concentration (SC) of free AA. Treatments were: high protein, 21.9% CP diet (HShp); and low protein, 13.5% CP diet supplemented with crystalline Lys, Thr, Met, Trp, His, Ile, Leu, Phe, and Val (HSaa). The HShp diet met or exceeded all AA requirements. The HSaa diet was formulated on the basis of ideal protein. Pigs were fed the same amount at 0700 and 1900 h during the 21-d study. Blood samples were collected at 1700 h (2.0 h before the evening meal), 2030 h, and 2130 h (1.5 and 2.5 h after the evening meal). At the end, all pigs were sacrificed to collect intestinal mucosa and a 5-cm section from each segment of small intestine from each pig. Villi measures, expression of AA transporters (y+L and B0) in mucosa, and SC of AA were analyzed. Ambient temperature fluctuated daily from 24.5 to 42.6 °C. Weight gain and G.F were not affected by dietary treatment. Villi height tended to be larger (P ≤ 0.10) and the villi height:crypt depth ratio was higher in duodenum and jejunum of pigs fed the HSaa diet (P < 0.05). Gene expression of transporter y+L in jejunum tended to be lower (P < 0.10) and transporter B0 in ileum was lower (P < 0.05) in HSaa pigs. Preprandial (1700 h) SC of Arg, His, Ile, Leu, Thr, Trp, Val was higher (P < 0.05), and Phe tended to be higher (P < 0.10) in HShp pigs. At 2030 h (1.5 h postprandial), serum Lys, Met, and Thr was higher in the HSaa pigs (P < 0.05). At 2130 h (2.5 h), Arg, His, Ile, Phe, and Trp was lower (P < 0.05), Met was higher (P < 0.05), and Lys tended to be higher (P < 0.10) in HSaa pigs. In conclusion, feeding HS pigs with low protein diets supplemented with free AA reduces the damage of the intestinal epithelia and seems to improve its absorption capacity, in comparison with HS pigs fed diets containing solely protein-bound AA. This information is useful to formulate diets that correct the reduced AA consumption associated with the decreased voluntary feed intake of pigs under HS.