Ionizing radiation (IR) is a curative treatment for many human malignancies, an important diagnostic modality, and a pivotal preparative regimen for bone marrow transplantation. On the other hand, IR is a potent damaging agent that can affect a variety of processes in directly exposed cells, in their descendents, and in neighboring un-irradiated naïve ‘bystander’ cells. Accumulation of DNA damage caused by IR in conjunction with disrupted cellular regulation processes can lead to genome instability in the germline, and therefore to transgenerational genome instability in offspring of exposed males. The exact mechanisms of IR-induced genome instability in directly exposed and in naïve bystander germ cells remain obscure, yet accumulating evidence points to the role of DNA damage and DNA methylation changes in genome instability development. In the current study, we used a well-established murine model to define the role of DNA methylation, DNA damage, as well as two important germline regulators of DNA methylation, Brother of the Regulator of Imprinted Sites (BORIS) and CCCTC binding factor (CTCF), in IR and bystander responses of the male germline. Here we report that irradiation leads to a significant accumulation of DNA damage in the exposed and bystander testis tissue, and to altered DNA methylation and dysregulated BORIS expression in the exposed testis tissue. The possible molecular mechanisms and biological consequences of the observed changes are discussed.