Abstract Thymocyte selection-associated HMG-box protein (TOX) is a nuclear DNA-binding factor that is expressed at discrete stages of T cell development in the thymus. We have previously reported that development of CD4 T cells, NKT cells and T regulatory cells is severely inhibited in TOX-deficient mice, as a result of a block in the completion of thymic positive selection. In contrast, CD8 T cells, γδT cells, and B cells develop in these animals. Here we document that there are other severe abnormalities in development of the immune system in the absence of TOX, including inhibition of the development of NK cells and loss of lymph nodes (LN). TOX-deficient bone marrow precursor cells fail to develop into NK cells under appropriate conditions in vitro, suggesting an intrinsic defect in hematopoiesis. Peripheral lymph nodes are undetectable in TOX-deficient mice, while the number and size of Peyer's patches are severely reduced. Bone marrow chimeras demonstrate that loss of LNs is not due to aberrant migration of lymphoid populations. Indeed, TOX-deficient mice have few phenotypically defined lymphoid tissue inducer cells, suggesting a developmental defect in organogenesis. We are currently investigating the mechanisms surrounding these phenotypes.