DNA methylation is crucial for normal development, proliferation, and proper maintenance of genome stability for a given organism. A variety of DNA damaging agents that are known to affect genome stability were also shown to alter DNA methylation patterns. We have recently pioneered the studies in the area of the radiation effects on DNA methylation, and found that radiation exposure led to substantial dose-dependent and tissue-specific DNA hypomethylation, which was much more pronounced in spleen and liver of female animals. The exact mechanisms of radiation-induced DNA hypomethylation are still to be uncovered. We have previously shown that one of those mechanisms may potentially be DNA repair related. Another possible mechanism may be linked to changes in the expression of DNA methyltransferases (DNMTs). In the current study, we examined the radiation-induced changes in expression of maintenance DNMT1, and de novo methyltransferases DNMT3a and DNMT3b in spleen and liver of irradiated animals. This was paralleled by the studies of acute and chronic IR-induced methylation changes in spleen and liver of intact animals, as well as in animals with altered sex hormone status. Here we report that radiation-induced DNA methylation changes correlated with radiation-induced alterations in expression of DNA methyltransferases. We present the data on tissue-specificity in radiation-induced expression of DNA methyltransferases, and prove that changes in the expression of de novo methyltransferases DNMT3a and DNMT3b are the most important in radiation-induced DNA methylation alterations. We also discuss the role of sex hormones, especially estrogen, in the generation of the sex-specific radiation-induced methylation changes.