Chronic exposure to arsenic in drinking-water damage to cognitive function, and nerve cells apoptosis is one of primary characteristic. The damage of mitochondrial structure and/or function is one of the main characteristics of apoptosis. Peroxisome proliferator activated receptor γ Coactivator α (PGC-1α) is involved in the regulation of mitochondrial biogenesis, energy metabolism and apoptosis. In this study, we aimed to study role of PGC-1α in sodium arsenite (NaAsO2)-induced mitochondrial apoptosis in rat hippocampal cells. We discovered that arsenic-induced apoptosis increased in rat hippocampus increased with NaAsO2 (0, 2, 10, and 50 mg/L, orally via drinking water for 12 weeks) exposure by TUNEL assay, and the structure of mitochondria was incomplete, swollen, lysosomes and lipofuscin increasing, and nuclear membrane shrunk observed by transmission electron microscope. Furthermore, NaAsO2 reduced levels of Bcl-2 and PGC-1α, increased the levels of Bax and Cytochrome C expression. Moreover, correlation analysis showed that brain arsenic content was negatively correlated with PGC-1α level and brain ATP content, respectively; PGC-1α level was negatively correlated with apoptosis rate; Brain ATP content was positively correlated with PGC-1α level; but no significant correlation between ATP content and apoptosis has been observed in this study. Taken together, the results of present study indicate that NaAsO2-induced mitochondrial pathway apoptosis is related to the reduction of PGC-1α, accompanied by ATP depletion.