Using flow cytometry, we quantified the number of micronucleated reticulocytes in peripheral blood of whole-body X-irradiated mice in order to evaluate the radiation sensitivity and the induced genomic instability of the hematopoietic system. An acute effect of radiation dose as small as 0.1 Gy was detectable 2 days after irradiation, and the radiation dose effect was significantly greater in BALB/c mice than in C57BL/6 mice, that is, 3.0- and 2.3-fold increases in frequencies of micronuclei were noted in the two groups of mice, respectively. Even 1 year after irradiation, mice irradiated with 2.5 Gy of X-rays showed significantly increased frequencies of micronucleated reticulocytes, that is, 1.6- and 1.3-fold increases in BALB/c and C57BL/6 mice, respectively. However, this delayed effect was not apparent when the same mice were analyzed for T-cell receptor mutant frequencies in splenocytes. A significant mouse strain difference in the delayed radiation effect on micronucleated reticulocyte frequencies was noted as well. The results indicate that delayed genomic effects of irradiation on the murine hematopoietic system can persist in vivo for prolonged periods, and that there are mouse strain differences in sensitivity to radiation-induced genomic instability.