In contrast to peripheral plasmacytoid DCs (pDCs), thymic pDCs constitutively express low levels of IFN‐α. This leads to induction of interferon secondary genes (ISGs) 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 pDCs, we found that thymic pDCs have a phenotype consistent with an “activated signature” including expression of TNF‐α and bone marrow stromal cell antigen 2 (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 pDCs. Further, we also show that BST2 is constitutively expressed 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 pDCs play an important role in the development of natural Treg cells.