The bystander effect is a phenomenon that occurs when exposed cells signal distress to their naïve, unexposed neighbors. It is now accepted as a ubiquitous consequence of radiation exposure. It is well documented to occur in cultured cells, 3D tissue models, and in organs and organisms. Notwithstanding, the exact mechanisms of the bystander effect remain unclear. Recent studies hinted that bystander effects may, in part, be distinct in males and females, and possibly mediated via short non-coding RNAs, specifically, microRNAs. MicroRNAs are small, abundant and capable of regulating the expression of a wide variety of targets. Yet, their roles in bystander effects have not been analyzed in detail. The mechanisms behind sex differences observed in in vivo bystander effects also remain to be uncovered. We hypothesized that the radiation-induced expression of microRNAs in exposed and bystander tissue may be distinct in males and females. Using a well-establish bystander mouse model when the animal's head is exposed, while the body is completely protected by a medical-grade shield, we have for the first time shown that radiation exposure triggers a significant and sex-specific deregulation of the microRNAome in the non-exposed bystander spleen. The altered miRNA levels were paralleled by sex-specific changes in the levels of the miRNA processing enzyme Dicer and components of the RNA-induced silencing complex (RISC). Sterilization of animals resulted in drastic microRNAome alterations and significantly affected radiation and bystander miRNA responses. Our data may provide a roadmap for further analysis of the role of microRNAome in genotoxic stress responses and may help us explain sex specificity of radiation-induced carcinogenesis.