In contrast to peripheral plasmacytoid dendritic cells (pDC), thymic pDC constitutively express low levels of IFN-α. This leads to induction of ISG in medullary thymocytes, raising the question whether IFN-α may play a role in T cell development. When characterizing further differences between peripheral and thymic pDC, we found that thymic pDC have a phenotype consistent with an “activated signature” including expression of TNF-α and BST2, but no expression of ILT7. Given that BST2 is induced by IFN-α and IFN-α secretion is controlled by interaction between ILT7 and BST2, this regulatory pathway is apparently lost in thymic pDC. Further, we also show that BST2 is expressed constitutively on a subset of medullary thymocytes at the mRNA and protein level reflecting a history of IFN-α transduced signals. The majority of BST2+ thymocytes express CCR5 rendering them prevalent targets for R5-tropic HIV infection. Moreover, BST2+ thymocytes express Foxp3 and CD25, consistent with the phenotype of natural Treg cells, and exert suppressive activity as they impair the proliferation of autologous CD3+ thymocytes. Collectively, our results suggest that low levels of IFN-α secreted by thymic pDC play an important role in the development of natural Treg cells.