Secondary brain damage plays a critical role in the outcome of patients with traumatic brain injury (TBI). The multiple mechanisms underlying secondary brain damage, including posttraumatic cerebral ischemia, glutamate excitotoxicity, oxidative stress, calcium overload and inflammation, are associated with increased mortality and morbidity after head injury. TBI is documented to have detrimental effects on mitochondria, such as alterations in glucose utilization and the depression of mitochondrial oxidative phosphorylation. Studies on mitochondrial metabolism have provided evidence for dysfunction of the cytochrome oxidase complex of the electron transport chain (complex IV) after TBI. A growing body of evidence indicates that cytochrome c oxidase is vital for mitochondrial oxidative phosphorylation. Therefore, this study aimed to detect the expression of cytochrome c oxidase (CO) mRNA in a rat weight-dropping trauma model and to clarify the differences between injured cortex (IC) and contralateral cortex (CC) after TBI. A total of forty-four rats were randomly assigned to 7 groups: control groups (n=4), sham-operated group (n=20), 6 h, 1 d, 3 d, 5 d and 7 d postinjury groups (n=4 for each group). The group consisted of sham-operated animals underwent parietal craniotomy without TBI. The rats in postinjury groups were subjected to TBI. The rats of control group were executed immediately without TBI or craniotomy after anesthesia. The brain-injured and sham-operated animals were killed on 6 h, 1 d, 3 d, 5 d and 7 d, respectively. Tissue sections from IC and CC were obtained and the expression of cytochrome c oxidase I, II, and III (CO I, II, III) mRNA, three mitochondrial encoded subunits of complex IV, were assessed by Real-time quantitative PCR. A reduction of CO I, II, and III mRNA expression was detected from IC and reduced to the lowest on 3 d. By contrast, the mRNA expression from CC suggested a slight elevation. The differences may indicate the degree of metabolic and physiologic dysfunction. Our results will better define the roles of gene expression and metabolic function in long-term prognosis and outcome after TBI. With a considerable understanding of post-injury mitochondrial dysfunction, therapeutic interventions targeted to the mitochondria may prevent secondary brain damage that leads to long-term cell death and neurobehavioral disability.