Heavy ion beam irradiation has promising effects on tumor therapy. Our previous study using the domesticated silkworm, Bombyx mori, showed that this irradiation could seriously damage larval hematopoietic organs but they would regenerate later. In the in vitro irradiation, most hemocytes died when hematopoietic organs and wing discs connected with epidermis were directionally irradiated from epidermis to hematopoietic organ and then cultured so as to exclude circulating hemocytes. A few hemocytes had escaped irradiation according to extremely low hematopoiesis in vitro. Almost no hemocytes could incorporate BrdU at 60 h after irradiation, with which living and proliferating hemocytes are also labeled. In the absence of circulating hemocytes, the irradiation-escaped hemocytes in the organs were not enough for cleaning all dead cells because lots of small dead bodies remained in situ post-irradiation. After irradiating hematopoietic organs in larvae (in vivo irradiation), only a few apoptotic cells were found when given the same length of recovery time, and most hemocytes maintained normal morphology. Many hemocytes incorporated BrdU when tested at the same time as the in vitro irradiation but this number was lower than that measured for control organs. Circulating hemocytes, labeled by fluorescent microbeads through phagocytosis before irradiation, were found to have invaded the in vivo irradiated hematopoietic organs where they help the irradiation-escaped hemocytes to clear dead cells in the process of regeneration. Hematopoiesis of the regenerated hematopoietic organs did not fully recover to the level of the control organs according to the number of hemocytes produced in tissue culture. Some of the released hemocytes obviously underwent apoptosis, suggesting a far-reaching bystander effect of carbon ion beams irradiation on hemocytes inside. From these results, it is suggested that, together with irradiation-escaped hemocytes, the invaded circulating hemocytes took part in the regeneration of heavy ion beams irradiated hematopoietic organs through the way of phagocytosis of injured hemocytes in vivo.