The objective of this study was to assess the effect of heat stress on the autophagy and apoptosis of the rumen, abomasum, duodenum, liver and kidney in calves. Two groups of Holstein male calves were selected with similar birth weights and health conditions. Heat stress (HT): Six calves (birth weight 42.2 ± 2.3) were raised from July 15 to August 19. Cooling (CL): Six calves (birth weight 41.5 ± 3.1 kg) were raised from April 10 to May 15. All the calves were euthanized following captive bolt gun stunning at 35 d of age. The expression of protein 1 light chain 3-Ⅱ (LC3-Ⅱ) and caspase3 in the rumen, abomasum, duodenum, liver and kidney were determined by western blotting. In addition, other possible relevant serum biochemical parameters were evaluated. Significant differences were observed in alkaline phosphatase (ALP), albumin (ALB) and glucose (Glu). The results showed that heat stress could increase the autophagy and apoptosis of the kidney, duodenum and abomasum. However, heat stress had no effect on the autophagy and apoptosis of the liver. Additionally, the expression of caspase-3 in the rumen in HT was significantly lower than that in CL. In conclusion, the effects of heat stress on autophagy and apoptosis are organ-specific. The results provide knowledge regarding autophagy and autophagy in calf heat stress management.