The major histocompatibility complex (MHC)-restricted presentation of self-peptides, generated from tissue-specific antigens, by thymic epithelial cells (TECs) is essential for development of central tolerance and for generation of the regulatory T-cell repertoire in the thymus. However, the mechanisms by which self-peptides are generated in and presented by TECs have not been well defined. To elucidate the processes involved in MHC class II-restricted presentation of selfpeptides by TECs, cortical and medullary TEC lines may be established from C57BL/6 mouse thymi. Localization of a variety of molecules, including the MHC class II molecules critically involved in the presentation of antigen by TECs, may be investigated by both immunofluorescence microscopy and Western blotting analyses. Our own studies using these approaches have demonstrated that such molecules are localized in the H2-DM⁺ lysosomal compartments isolated from both cortical and medullary TECs.