The autoimmune regulator Aire is expressed in a small proportion of medullary thymic epithelial cells (mTECs) and is crucial in the induction of central T cell tolerance. The origin and development of Aire⁺ mTECs, however, are not well understood. Here we demonstrate that the tight-junction components claudin-3 and claudin-4 (Cld3,4) were 'preferentially' expressed in Aire⁺ mTECs. In early ontogeny, Cld3,4^hi TECs derived from the most apical layer of the stratified thymic anlage first expressed known mTEC markers such as UEA-1 ligand and MTS10. We provide evidence that such Cld3,4^hi UEA-1⁺ TECs represented the initial progenitors specified for Aire⁺ mTECs, whose development crucially required NF-κB-inducing kinase and the adaptor molecule TRAF6. Our results suggest that Aire⁺ mTECs represent terminally differentiated cells in a unique lineage arising during thymic organogenesis.