Although it is well known that in vivo radiation depletes immune cells via the Bcl-2 apoptotic pathway, a more nuanced analysis of the changes in the balance of immune-cell subsets is needed to understand the impact of radiation on immune function. We show the balance of T-cell subsets changes after increasing single doses of total body irradiation (TBI) or after fractionated irradiation of the lymphoid tissues (TLI) of mice due to differences in radioresistance and Bcl-2 expression of the NKT-cell and non-NKT subsets to favor CD4(+)Bcl-2(hi) NKT cells. Reduction of the Bcl-2(lo) mature T-cell subsets was at least 100-fold greater than that of the Bcl-2(hi) subsets. CD4(+) NKT cells upregulated Bcl-2 after TBI and TLI and developed a Th2 bias after TLI, whereas non-NKT cells failed to do so. Our previous studies showed TLI protects against graft versus host disease in wild-type, but not in NKT-cell-deficient mice. The present study shows that NKT cells have a protective function even after TBI, and these cells are tenfold more abundant after an equal dose of TLI. In conclusion, differential expression of Bcl-2 contributes to the changes in T-cell subsets and immune function after irradiation.