The long-term genetic consequences of chronic exposure to low-dose irradiation constitutes a major concern to the general public and research community, especially as chronic radiation has recently been proven to be much more mutagenic and carcinogenic than previously thought. Here we report the results of the first ever comparison of the effects of acute and chronic whole body low-dose radiation exposure on global gene expression. We found a substantial difference between males and females in the expression of genes involved in signaling, growth control, transcription and other pathways upon acute and chronic radiation exposure. Specifically, we found sex differences in the expression of genes coding for G protein-coupled receptors and nuclear receptors. We also found different induction of PKCdelta, PKCbeta and PKCmu, members of PKC signaling pathway as well as in TGF and WNT signaling in males and females. Very pronounced difference, that was confirmed on the level of protein, was observed in the expression of WNT5A that plays an important role in carcinogenesis and muscle regeneration. WNT5A expression was significantly elevated only in chronically exposed females. We also provide the first evidence of the effect of ionizing radiation on the estrogen receptor in females. Repetitive irradiation of muscle tissue has been linked to development of rhabdomyosarcoma (RMS), which, enigmatically, occurs more frequently in males. Our data may be used to study possible mechanisms of RMS development upon chronic radiation exposure. They may provide some clues about the molecular background of the sex differences of RMS occurrence and may in the future lead to the discovery of new biomarkers for RMS predisposition in the irradiated tissue. Overall, differences in male and female responses to acute and chronic low-dose radiation obtained by this study were more drastic than we could have predicted. If confirmed in other experimental systems, these findings could potentially lead to fundamental changes in radiation safety regulations.