This study aims at elucidating the cellular responses induced by energy deposition in the cell nucleus or cytoplasm in the low-dose (< 1 Gy) region. We compared the survival fraction of V79 cells irradiated with X-ray microbeams of different sizes. Entire cells or cell nuclei were targeted with 5.35 keV monochromatic X-ray microbeams using a synchrotron radiation (SR) X-ray microbeam irradiation apparatus. Using a threshold of 30 cells/colony after 60 h of incubation, conditions that had been proven to give results equivalent to those of the conventional method, we determined the survival fraction of the microbeam-irradiated cells. When cell nuclei were irradiated with 10 x 10 microm (2) X-ray beams, the survival fraction was almost the same as that obtained with 50 x 50 microm (2) beams except in the low-dose region. In the low-dose region irradiated with 10 x 10 microm (2) beams, hyper-radiosensitivity (HRS) was clearly observed in the nucleus-irradiated cells, and the survival curve exhibited a minimum of about 60% at 0.5 Gy. This may be the most distinct HRS reported thus far when an asynchronous population is used. Difference in observed HRS phenomena is solely due to the irradiated part in the cell. These results suggest that energy deposition in the cytoplasm might suppress the HRS.