Poly(ADP-ribose) polymerase-1 knockout (Parp-1(-/-)) mice show increased frequency of spontaneous liver tumors compared to wild-type mice after aging. To understand the impact of Parp-1 deficiency on mutations during aging, in this study, we analyzed spontaneous mutations in Parp-1(-/-) aged mice. Parp-1(-/-) mice showed tendencies of higher mutation frequencies of the red/gam genes at 18 months of age, compared to Parp-1(+/+) mice, in the liver and brain. Complex-type deletions, accompanying small insertion were observed only in Parp-1(-/-) mice in the liver and brain. Further analysis in the liver showed that the frequency of single base deletion mutations at non-repeat or short repeat sequences was 5.8-fold higher in Parp-1(-/-) than in Parp-1(+/+) mice (p<0.05). A 3.2-fold higher tendency of the deletion frequency of two bases or more was observed in Parp-1(-/-) mice compared to Parp-1(+/+) mice (p=0.084). These results support the model that Parp-1 is involved in suppressing imprecise repair of endogenous DNA damage leading to deletion mutation during aging. The mutation frequencies of the gpt gene in the brain were found to be 3-fold lower in Parp-1(-/-) than in Parp-1(+/+) mice at 4 months of age (p<0.01), implying that Parp-1 may be positively involved in imprecise DNA repair in the brain. On the other hand, the frequencies of gpt mutation showed an increase at 18 months of age in the Parp-1(-/-) (p<0.05) but not in Parp-1(+/+) brains, suggesting that Parp-1 deficiency causes an increase of point mutations in the brain by aging.