Simple SummaryOther than DNA damage, it has become clear that ionizing radiation can also induce epigenetic effects. Thus, intergenerational effects from chronic low-dose exposures are possible concerns. It is important to elucidate the effects of radiation on germ cell maturation, fertilization and embryonic development. We analyzed global DNA methylation patterns in the testes and expression of Izumo1 in the testes and Izumo1r (Izumo1 receptor) in the ovaries of mice after neonatal acute high-dose radiation (HDR) and chronic low-dose radiation (LDR). The results of global DNA methylation patterns in the testis showed that the LDR group maintained its DNA methylation level, while the HDR group showed decreased DNA methylation levels with age. The expression level of Izumo1 in the testis recovered after the end of irradiation in the LDR group, while it remained low regardless of age in the HDR group. Although the expression of Izumo1r in the ovary decreased with age in the LDR group, it remained low in the HDR group. Our results indicate that LDR can induce different DNA methylation patterns, and both low- and high-dose radiation before sexual maturity might affect gametogenesis and fertility.The intergenerational effects from chronic low-dose exposure are matters of concern. It is thus important to elucidate the radiation-induced effects of germ cell maturation, fertilization and embryonic development. It is well known that DNA methylation levels in CpG sites in gametes are reprogrammed in stages during their maturity. Furthermore, the binding of Izumo on the surface of sperm and Juno on the surface of oocytes is essential for fertilization. Thus, there is a possibility that these genes are useful indicators to evaluate fertility in mice after irradiation exposure. Therefore, in this study, we analyzed global DNA methylation patterns in the testes and gene expression of Izumo1 and Izumo1r (Juno) in the gonads of mice after neonatal acute high-dose ionizing radiation (HDR) and chronic low-dose ionizing radiation (LDR). One-week-old male and female mice were irradiated with a total dose of 4 Gy, with acute HDR at 7 days at a dose rate of 30 Gy/h and LDR continuously at a dose rate of 6 mGy/h from 7 to 35 days. Their gonads were subsequently analyzed. The results of global DNA methylation patterns in the testes showed that methylation level increased with age in the control group, the LDR group maintained its DNA methylation level, and the HDR group showed decreased DNA methylation levels with age. In the control group, the gene expression level of Izumo1 in the testis did not show age-related changes, although there was high expression at 100 days of age. However, in the LDR group, the expression level recovered after the end of irradiation, while it remained low regardless of age in the HDR group. Conversely, gene expression of Izumo1r (Izumo1 receptor) in the ovary decreased with age in the control group. Although the gene expression of Izumo1r decreased with age in the LDR group, it remained low in the HDR group. Our results indicate that LDR can induce different DNA methylation patterns, and both high- and low-dose radiation before sexual maturity might affect gametogenesis and fertility.