Due to the immunomodulatory properties of MHC Ib molecules and due to the relevance of Aire and FOXP3 in self-tolerance, it is hypothesized that changes in expression of these molecules in thymus during antiviral responses could be related to (i) alterations in thymic function, resulting in a defective PGE and negative selection, (ii) modifications in the regulatory T cell repertoire, and (iii) appearance of autoimmune disorders [7, 16, 19]. Here, FOXP3 is linked to Autoimmunity.