Autoimmune diseases are frequently characterized by the presence of autoantibodies directed against nucleic acidprotein complexes present in the nucleus of the cell. The mechanisms by which these autoantigenic molecules escape immunological tolerance are largely unknown, although a number of recent observations suggest that modified selfproteins generated during apoptosis may play an important role in the development of autoimmunity. It has been hypothesized that the recognition of these modified selfproteins by the immune system may promote autoantibody production. While apoptosis is specifically characterized by posttranslational modification of proteins, recent findings also show that nucleic acids are modified. This review summarizes the specific cleavages of some of these key nucleic acids, i.e. chromosomal DNA, ribosomal RNA and small structural RNAs (U1 snRNA, Y RNA), in apoptotic cells.