Many tissue-specific antigens are expressed in specialized cells called peripheral antigen-expressing cells (PAE) in the thymus and can induce central tolerance. While thymic medullary epithelial cells are the prototypic PAE that express peripheral antigens via an aire-dependent mechanism, some studies also describe bone marrow (BM)-derived dendritic cells (DC) and macrophages as PAE in both the thymus and secondary lymphoid organs. However, the role of these cells in development of tolerance to tissue-specific antigens has not been elucidated. Here we use BM radiation chimeric mice to study the existence of hematopoietic PAE and their contribution to tolerance to tissue-specific antigens. Our results reveal that BM-derived PAE exist in both central and secondary lymphoid organs and that the expression of peripheral antigens in the BM-derived cells does not correlate with aire expression. Using double-transgenic mice expressing TCR specific for a model antigen expressed under the control of a prostate-specific promoter, we show that expression of self antigen in PAE of non-hematopoietic origin is both necessary and sufficient to induce clonal deletion. Surprisingly, while BM-derived PAE fail to induce clonal deletion, they do cause the activation-induced cell death of autoreactive cells in the secondary lymphoid organs. Thus, BM-derived PAE have a distinct function in the maintenance of tolerance to tissue-specific antigens.