Proton radiation (PR) therapy offers a number of potential advantages over conventional (photon) gamma-radiation (GR) therapy for cancer, due to a more localized delivery of the radiation dose. However, the pathophysiological effects following PR-exposure are less well characterized than those of GR-exposure and the molecular changes associated with the acute apoptotic effects in mice in vivo following PR have not been elucidated. Previous studies have estimated the RBE of protons for various in vivo and in vitro endpoints at between 1.1 and 1.3. We assumed an RBE of 1.1 for the endpoints to be evaluated in these studies. Based on this assumption, ICR mice were treated with whole-body doses of GR (1.1 and 7.0 Gy) and PR (1.0 and 6.4 Gy) that were expected to represent RBE-weighted doses. The bone marrow, thymus, spleen and GI-tract were isolated and processed for histology and immunohistochemistry. The apoptotic responses varied greatly between GR and PR in a tissue- and dose-dependent manner. Surprisingly,cell death in the splenic white pulp was consistently lower in PR-treated animals compared to animals treated with GR. This was in spite of an increased presence of damaged DNA following PR as determined by staining for gammaH2AX and phospho-ATM. Interestingly, both PR and GR triggered nuclear accumulation of p53 and no significant differences were found in the majority of the known pro-apoptotic p53-target genes in the spleens of treated mice. However, GR uniquely triggered a pro-apoptotic expression profile including expression of the pro-apoptotic, p53- and interferon stimulated target gene Bcl-G. In contrast to PR, GR may, in a cell type specific manner, trigger a more diverse non-random stress-response that mediates apoptosis partially independent of the extent of DNA damage.