We have investigated the role of mitochondria on the development of indomethacin (a non-steroidal anti-inflammatory drug)-induced gastric mucosal apoptosis and associated gastropathy in rat. Transmission electron microscopic studies indicate that indomethacin damages mitochondrial ultrastructure and causes mitochondrial dysfunction as evident from decreased stage-3 respiration, dehydrogenase activity, and transmembrane potential (⌬ m ). Mitochondrial pathology is associated with increased generation of intra-mitochondrial-reactive oxygen species, such as O 2 . , H 2 O 2 and ⅐OH, leading to oxidative stress. O 2 . is the most effective to damage mitochondrial aconitase, leading to the release of iron from its iron-sulfur cluster. The released iron, by interacting with intra-mitochondrial H 2 O 2 , forms ⅐OH. Immunoprecipitation of mitochondrial aconitase and subsequent Western immunoblotting indicate carbonylation of aconitase along with the loss of activity in vivo after indomethacin treatment. The release of iron has been documented by fluorescence imaging of mucosal cells by using Phen Green SK, a specific probe for chelatable iron. Interestingly, intra-mitochondrial ⅐OH generation is crucial for the development of mitochondrial pathology and activation of mitochondrial death pathway by indomethacin. Scavenging of ⅐OH by dimethyl sulfoxide or ␣-phenyl-n-tert-butylnitrone, a spin-trap, prevents indomethacin-induced mitochondrial ultrastructural changes, oxidative stress, collapse of ⌬ m , and mitochondrial dysfunction. The scavengers also restore indomethacin-induced activation of caspase-9 and caspase-3 to block mitochondrial pathway of apoptosis and gastric mucosal damage. This study, thus, reveals the critical role of O 2 . -mediated mitochondrial aconitase inactivation to release intra-mitochondrial iron, which by generating ⅐OH promotes gastric mucosal cell apoptosis and gastropathy during indomethacin treatment.Non-steroidal anti-inflammatory drugs (NSAIDs) 2 are one of the most commonly prescribed drugs in the world to treat pain and inflammation (1). Everyday about 30 million people consume NSAIDs (1). These drugs are gaining enormous interest for cancer therapy as well (2, 3), as they are potent inducers of apoptosis and inhibitors of cell proliferation (4). However, long term use of NSAIDs is associated with severe gastropathy (1, 5) that may arise from induction of gastric mucosal cell apoptosis (6 -9). NSAIDs induce apoptosis in vitro in varieties of cancer cells such as esophageal (10) and gastric adenocarcinoma cells (11), lung carcinoma cells (12), myeloid leukemia cells (13), and prostate carcinoma cells (3). NSAIDs also induce apoptosis in normal gastric mucosal cells (7, 9), hepatocytes (14), and chondrocytes (15). Up-regulation of proapoptotic Bax, Bak, and down-regulation of antiapoptotic Bcl-2, BclxL, are found to occur in NSAID-induced gastric mucosal apoptosis (7). Up-regulation of Bax as well as down-regulation of Bcl-2 are also observed in indomethacin-induced chronic myeloid leukemic c...