Since 1988 several research groups have reported greater levels of oxidative damage in mitochondrial DNA than in nuclear DNA, while others have suggested that the greater damage in mtDNA might be due to artifactual oxidation. The popular theory that mtDNA is more heavily damaged in vivo than nDNA does not stand on firm ground. Using an improved GC-MS method and pure mtDNA, our analyses revealed that the damage level in mtDNA is not higher, and may be somewhat lower, than that in nDNA.