T lymphocytes express receptors (T-cell receptor) that are not only specific for antigenic peptide but also molecules encoded by the major histocompatibility complex (MHC) that present peptide on the surface of cells (MHC-restricted antigen recognition). However, the vast majority of T cells are tolerant to their own MHC molecules and do not give rise to autoimmune disease. This MHC-restricted, but tolerant, repertoire of T cells is determined by selection triggered by the appropriate recognition of peptide/MHC on thymic stromal cell by immature thymocytes. We have developed a fetal thymus organ culture (FTOC) system based on transporter associated with antigen processing (TAP) 1-deficient mice to examine the role of peptide/MHC in triggering the differentiation of T cells restricted to class I MHC (positive selection). We also describe an FTOC system to study central T-cell tolerance, which occurs through clonal deletion in the thymus (negative selection).