In mammalian cells, more than one genome has to be maintained throughout the entire life of the cell, one in the nucleus and the other in mitochondria. It seems likely that the genomes in mitochondria are highly exposed to reactive oxygen species (ROS) as a result of their respiratory function. Human MTH1 (hMTH1) protein hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP, 8-oxo-dATP, and 2-hydroxy (OH)-dATP, thus suggesting that these oxidized nucleotides are deleterious for cells. Here, we report that a single-nucleotide polymorphism (SNP) in the human MTH1 gene alters splicing patterns of hMTH1 transcripts, and that a novel hMTH1 polypeptide with an additional mitochondrial targeting signal is produced from the altered hMTH1 mRNAs; thus, intracellular location of hMTH1 is likely to be affected by a SNP. These observations strongly suggest that errors caused by oxidized nucleotides in mitochondria have to be avoided in order to maintain the mitochondrial genome, as well as the nuclear genome, in human cells. Based on these observations, we further characterized expression and intracellular localization of 8-oxoG DNA glycosylase (hOGG1) and 2-OH-A/adenine DNA glycosylase (hMYH) in human cells. These two enzymes initiate base excision repair reactions for oxidized bases in DNA generated by direct oxidation of DNA or by incorporation of oxidized nucleotides. We describe the detection of the authentic hOGG1 and hMYH proteins in mitochondria, as well as nuclei in human cells, and how their intracellular localization is regulated by alternative splicing of each transcript.