Valpha14 invariant (Valpha14i) NK T cell development is unique from mainstream T cell selection, and the polygenic factors that influence NK T cell ontogeny are still unclear. In this study, we report the absence of Valpha14i NK T cells in B6.IFN-alphabetaR1-/- male mice, whereas both the conventional T and NK cell populations are relatively unaffected. The lack of Valpha14i NK T cells in the B6.IFN-alphabetaR1-/- males is not due to an insufficient level of CD1d1 or a defect in CD1d1-Ag presentation, but it is intrinsic to the male Valpha14i NK T cells. This surprising defect displays >or=99% penetrance in the male population, whereas female mice remain unaffected, indicating the deficiency is not X linked. Analysis of the Valpha14i NK T cell compartment in B6.Tyk2-/-, B6.STAT1-/-, 129.IFN-alphabetaR1-/-, and B6.IFN-alphabetaR1-/+ mice demonstrate that the deficiency is linked to the Y chromosome, but independent of IFN-alphabeta. This is the first study demonstrating that Y-linked genes can exclusively impact Valpha14i NK T development and further highlight the unique ontogeny of these innate T cells.