To our knowledge the mechanism of neurodegeneration in the overactive bladder remains unknown. We examined mitochondrial integrity and searched for markers of oxidative neural injury in the ischemic overactive bladder. A rabbit model of overactive bladder was developed by inducing moderate pelvic ischemia. After 16 weeks cystometrograms and blood flow recordings from overactive bladders were compared with those in age matched controls. Bladder tissues were processed to assess oxidative products, oxidative stress sensitive genes and nerve fiber density using enzyme immunoassay, quantitative real-time polymerase chain reaction and immunohistochemical staining, respectively. Tissue ultrastructure was examined by transmission electron microscopy. Ischemia increased spontaneous bladder contractions and led to cyclic ischemia-reperfusion. Tissue levels of oxidative and nitrosative products, and oxidative stress sensitive genes encoding superoxide dismutase and aldose reductase were up-regulated in the overactive bladder. Transmission electron microscopy of overactive bladder tissues showed mitochondria with distinctive morphological features, characterized by swollen membranes, decreased granules, a total loss of granules and sporadic membrane damage. These changes were associated with sporadic loss of epithelial mucosal membrane, twisted smooth muscle cells, diffused vacuolization and marked neurodegeneration. Our findings suggest free radical mediated ultrastructural damage and neurodegeneration in the overactive bladder. Overactivity associated mitochondrial stress may have a central role in epithelial damage, smooth muscle cell injury and neurodegeneration. Superoxide dismutase and aldose reductase up-regulation in the overactive bladder imply intrinsic defensive reaction against free radicals that apparently fails to prevent oxidative damage and neurodegeneration. Therapeutic strategies targeting basic mitochondrial processes such as energy metabolism or free radical generation may help better manage wall degeneration and neuropathy in the overactive bladder.