Humans are occasionally exposed to extreme environmental heat for a prolonged period of time. Here, we investigated testicular responses to whole-body heat exposure by placing mice in a warm chamber. Among the examined tissues, the testis was found to be most susceptible to heat stress. Heat stress induces direct responses within germ cells, such as eukaryotic initiation factor 2α phosphorylation and stress granule (SG) formation. Prolonged heat stress (42°C for 6 hr) also disturbed tissue organization, such as through blood-testis barrier (BTB) leakage. Germ cell apoptosis was induced by heat stress for 6 hr in a cell type- and developmental stage-specific manner. We previously showed that spermatocytes in the early tubular stages (I-VI) form SGs for protection against heat stress. In the mid-tubular stages (VII-VIII), BTB leakage synergistically enhances the adverse effects of heat stress on pachytene spermatocyte apoptosis. In the late tubular stages (IX-XII), SGs are not formed and severe leakage of the BTB does not occur, resulting in mild apoptosis of late-pachytene spermatocytes near meiosis. Our results revealed that multiple stress responses are involved in germ cell damage resulting from prolonged heat stress (42°C for 6 hr).