The objective of this study was to determine the relative susceptibilities to the damaging effects of hydrogen peroxide of DNA in the mitochondrial and nuclear compartments of two murine germ cell lines. We used a quantitative polymerase chain reaction assay (QPCR) to measure gene- and mitochondrial-specific DNA damage and examined for the presence of alkali-labile sites using alkaline gel electrophoresis. No DNA damage was observed in a nuclear gene (beta-globin) in response to hydrogen peroxide treatment. In addition, no increase in alkali-labile sites was observed. However, mitochondrial DNA suffered extensive damage which increased in a dose-dependent manner. These results demonstrate that the nuclear DNA in these germ cell lines is relatively resistant to peroxide-mediated DNA damage, and that mitochondrial DNA is a sensitive biomarker for oxidative stress in these cells.