Large-scale deletions of mitochondrial DNA (mtDNA) have been associated with aging and disease in post-mitotic tissues. These post-mitotic tissues, including skeletal muscle, heart and brain, are heavily dependent on intact functional mitochondria. The cochlear tissues are known to contain an abundance of mitochondria. This observation stimulated a search for mtDNA deletions in the cochlea and its elements using a sensitive nested PCR methodology and long range PCR to explain the functional deficits observed in age-related hearing loss. The presence of the so-called "common" deletion (CD) was detected in cochlear tissue from two individuals with age-related hearing loss, 73 and 78 years of age. Three additional deletions, that to our knowledge have not been previously reported, were also identified in these two individuals, including a 5354 bp deletion flanked with a 3 bp repeat, a 9682 bp deletion flanked by a 10 bp repeat and a 5142 bp deletion without a flanking repeat. The 9682 and 5142 bp deletions were also detected in an individual 39 years of age with normal hearing, however, these two deletions were not detected in a normal hearing individual 9 years of age. In contrast, the 5354 bp deletion was detected in all four of the individuals studied. To localize the deletions within the cochlea, the cochlear elements were removed by laser capture microdissection (LCM) and the mtDNA from these tissues was studied. The 5142 and 5354 bp deletions were detected in the organ of corti, spiral ligament, and ganglion cells, but not in the stria vascularis. These findings correlate with the reduction in the number of spiral ganglion cells and outer hair cells, and the normal stria vascularis volume observed in this individual. All four of these deletions involve the cytochrome c oxidase (COX) subunit III gene, encoded by mtDNA. These observations suggest that multiple mtDNA deletions may contribute to a deficit in mitochondrial function in the cochlea and result in hearing loss if a level of physiological significance is reached.