T cell receptor transgenic mice have been a valuable tool in the study of the immune system, from development to selection to tolerance or pathogenesis. In this manuscript we review the T cell receptor transgenic mouse lines with specificity for self antigens that have been reported before August 2003. Many such lines have been generated, which have been instrumental in our understanding of, among other aspects, the role regulatory T cells in preventing autoimmunity, the role of microbes in modifying its outcome, the influence of the genetic background, the importance of regional differences in self-antigen concentration, and the importance of differences in antigen deposition between different tissues.