Controlled cortical impact results in altered mitochondrial homeostasis in tissues ipsilateral to injury. Rats were subjected to either sham or controlled cortical impact treatment. PGC-1α messenger RNA expression was determined by reverse-transcriptase polymerase chain reaction (PCR) using tubulin as a control gene. Mitochondrial DNA copy number was determined by quantitative PCR, using ND1 for the mitochondrial gene and actin for the nuclear control gene. These markers were measured in the ipsilateral cortex and striatum at post-operative days 1 (A and D), 3 (B and E), and 6 (C and F). Values reported as mean ± SEM. n > 4, *p < 0.05. PGC-1α, peroxisome proliferator-activated receptor gamma coactivator 1-alpha; POD, post-operative day; SEM, standard error of the mean; TBI, traumatic brain injury.