It is well known that environmental factors such as chemicals and radiation cause DNA damage. In contrast, the consequences of bacterial infection on the integrity of host DNA are poorly understood. We show that two pathogens (Helicobacter pylori and Enterococcus faecalis) are implicated in the induction of genomic instability in both nuclear and mitochondrial DNA (mtDNA) of gastric epithelial cells. Instability in nuclear DNA is coupled to down-regulation of central DNA repair activities that includes DNA mismatch repair (MMR). By down-regulating MMR pathways, bacterial infections have the potential to inflict direct changes in the DNA of the host, such as oxidative damage, methylation, chromosomal instability, microsatellite instability, and mutations. Interestingly, bacterial infections generate instability in mtDNA by lowering mtDNA content as well as by decreasing complex I activity. Based on our results, we propose that bacterial infections promote genomic instability by at least three different mechanisms: (1) by a combination of increased endogenous DNA damage and decreased repair activities; (2) by induction of mutations in the mtDNA; and (3) by the generation of a transient mutator phenotype that induces mutations in the nuclear genome.