The role of reactive oxygen-induced oxidative damage to lipids (i.e., lipid peroxidation, LP) and proteins has been strongly supported in previous work. Most notably, a number of free radical scavengers and lipid antioxidants have been demonstrated to be neuroprotective in traumatic brain injury (TBI) models. However, the specific sources of reactive oxygen species (ROS), the time course of oxidative damage and its relationship to post-traumatic neurodegeneration in the injured brain have been incompletely defined. The present study was directed at an investigation of the role of the ROS, peroxynitrite (PON), in the acute pathophysiology of TBI and its temporal relationship to neurodegeneration in the context of the mouse model of diffuse head injury model. Male CF-1 mice were subjected to a moderately severe head injury and assessed at 1-, 3-, 6-, 12-, 24-, 48-, 72, 96- and 120-h post-injury for neurodegeneration using quantitative image analysis of silver staining and semi-quantitative analysis of PON-mediated oxidative damage to proteins (3-nitrotyrosine, 3-NT) and lipids (4-hydroxynonenal, 4-HNE). Significant evidence of silver staining was not apparent until 24-h post-injury, with peak staining seen between 72- and 120-h. This time-course of neurodegeneration was preceded by intense immunostaining for 3-NT and 4-HNE, which occurred within the first hour post-injury. The time course and staining pattern for 3-NT and 4-HNE were similar, with the highest staining intensity noted within the first 48-h in areas surrounding trauma-induced contusions. In the case of 3-NT, neuronal perikarya and processes and microvessels displayed staining. The temporal and spatial coincidence of protein nitration and LP damage suggests that PON is involved in both. However, lipid-peroxidative (4-HNE) immunoreactivity was broader and more diffuse than 3-NT, suggesting that other reactive oxygen mechanisms, such as iron-dependent LP, may also contribute to the more widespread 4-HNE immunoreactivity. This indicates that optimal pharmacological inhibition of post-traumatic oxidative damage in TBI may need to combine two functionalities: one to scavenge PON or PON-derived radicals, and the second to inhibit LP caused by multiple ROS species.