Mitochondrial transcription factor A (Tfam) has a key role in keep of copy numbers and transcription activity of mtDNA. The object of the recent study was to determine the effect of exercise training on serum levels and gene expression of mitochondrial transcription factor A and PGC1α in hippocampus of male rats. In the present study 20 Wistar rats were divided into training and control groups. Training protocol was done 60 min in each session for four sessions in each week. Training group was carried out 15 × 4 min bouts of training with 85 to 90% of VO2max that sustained with three min recovery with 70% of VO2max. PGC1α and Tfam and their gene translations were evaluated by commercial kits and Real-Time PCR method, respectively. Results illustrated that VO2max and serum levels of biomarkers of mitochondrial biogenesis were significantly increased (p<0.05). Also, PGC1α and Tfam gene translations in hippocampus were significantly increased (p<0.05). It seems that, the present three-week training protocol has competency to increase in both hippocampus and serum levels of PGC1α and Tfam in male rats. Likewise, there is a likelihood that significant increase of Tfam is due to meaningful vicissitudes of PGC1α.