Radiation-induced bystander effects are the biological responses exhibited by cells adjacent to cells that have been traversed by charged particles. Using a synchrotron X-ray microbeam irradiation system, we irradiated five cells in two different ways: by targeting the nuclei with 10 µm × 10-µm 5.35 keV X-ray beams and by irradiating the whole cells with 50 µm × 50-µm 5.35 keV X-ray beams. Then we measured the clonogenic survival of the bystander cells. When only the nuclei were irradiated, a parabolic enhancement of bystander cell death was observed in a dose-dependent manner in the low-dose region around 1 Gy. In contrast, the surviving fraction of bystander cells decreased monotonically when whole cells were irradiated. Addition of carboxy-PTIO, a specific scavenger of nitric oxide (NO), suppressed bystander cell death in both cases. These results indicate that NO is a mediator in the induction of the parabolic and monotonic types of bystander cell death. Moreover, from the spatial analysis, we found that the parabolic type of bystander cell death was induced primarily within 1 mm of irradiated cells. Our findings demonstrate that the induction of bystander cell death depends on the sites of energy deposition in irradiated cells.