Elimination of self-reactive T lymphocytes occurs during T-cell development in the thymus by a process known as negative selection. The mechanism that drives negative selection is apoptosis. To identify genes that regulate apoptosis in the mouse thymus, a library of negatively selected T cells was constructed and, by subtractive screening, several differentially regulated genes were isolated. Two transcripts that are repressed during cell death were identified, in addition to two induced transcripts. Further experiments demonstrated that cell death in thymocytes can occur via several induction pathways and each pathway appears to be regulated by a unique cascade of genes.