Formation of l-isoaspartyl (isoAsp) peptide bonds is a major source of protein damage in vivo and in vitro. Accumulation of isoAsp in cells is limited by a ubiquitous repair enzyme, protein l-isoaspartyl methyltransferase (PIMT). Reduction of PIMT activity in mouse brain or rat PC12 cells leads to a dramatic and selective accumulation of isoAsp sites in histone H2B. To learn more about the mechanism and specificity of isoAsp formation in histones, we purified mononucleosomes from rat liver and chicken erythrocytes and subjected them to in vitro aging for 0-16 days. In rat nucleosomes, the pattern of isoAsp accumulation duplicated that observed in vivo; only H2B accumulated significant isoAsp that we have now localized to the Asp25-Gly26 bond in the N-terminal tail. In chicken nucleosomes, isoAsp accumulated mainly in histone H2A and, to a lesser extent, in histone H2B. Minor sequence differences are consistent with the species-specific patterns of isoAsp accumulation and suggest that, in chicken, isoAsp occurs at the Asp121-Ser122 bond in the flexible C-terminal tail of H2A and at the Asp26-Lys27 bond in the N-terminal tail of H2B. The aging-induced accumulation of isoAsp in rat and chicken nucleosomes is repaired upon incubation of the damaged nucleosomes with PIMT and AdoMet. Our findings suggest that in vivo generation of isoAsp sites in histones occurs as a self-catalyzed process at the level of the nucleosome and is driven by the same structural features that have been shown to promote isoAsp formation in purified proteins and synthetic peptides.