Lipids are central to brain structure and function as brain has a remarkably high lipid content. Among different lipid classes in the brain, phospholipids play essential structural roles and act as important signaling molecules for neuronal health and disease. Acute brain injury has been shown to alter phospholipids primarily by oxidation upon trauma or ischemia/reperfusion. Although initial studies ascribed phospholipid oxidation to random free radical mediated events, recent advancements in liquid chromatography-mass spectrometry based oxidative lipidomics analyses have shown that contribution of enzymatic lipid peroxidation is the major pathogenic mechanism of phospholipid oxidation after acute brain injury. We have shown that cardiolipin (CL), a mitochondria unique phospholipid, is selectively oxidized after trauma or global ischemia of the brain. CL oxidation is a result of transmigration of CL from the inner to the outer mitochondrial membrane with resultant complex formation of CL with cytochrome c. The CL/cytochrome c complex utilizes hydrogen peroxide as the source of oxidizing equvalents to oxidize CL. Hydrolysis of oxidized CL by calcium-independent phospholipase A2 leads to a novel mitochondrial lipid signaling pathway by formation of monolyso-CL and oxidized free fatty acids as signaling lipid mediators after injury. Therapies using mitochondria targeted electron scavengers, hemigramicidin nitroxides, attenuate CL oxidation, neuronal death, and improve histological and neurocognitive outcome after acute brain injury. These data show that CL oxidation and subsequent hydrolysis represent a previously unidentified pathogenic mechanism of acute brain injury and a clinically relevant therapeutic target.