Background/Aims: Juglone, as a naphthoquinone, has been shown to have cytotoxic and apoptotic effects in various cancer cells and besides this effects it was reported to have anti-invasive and anti-metastatic effects in PANC-1 and BxPC-3 cells in our previous studies. In this study, we investigated the effects of juglone on GRP75, TFAM and mTOR genes encoding key proteins associated with mitochondrial biogenesis and activation in PANC-1 and BxPC-3 pancreatic cancer cells since mitochondria have central roles in cancer cell survival, metastasis and therapeutic resistance. Methods: In our study; 5, 10, 15 and 20 μM juglone doses were selected as the application doses considering the IC50 value determined after MTT test results and the expressions of the target genes were analyzed by qPCR method after application of juglone doses for 24 hours. Results: Our study results revealed that juglone had an opposite and strong effects on mTOR expression in both cell lines. Conclusion: Our findings suggest that juglone has a developable potential and is a promising theurapeutic agent to develop new strategies for the battle with cancer with those effects on mTOR gene which plays a central role in cellular homeostasis and several cellular events including cell growth, survival and metabolism.