Background: Cancer stem cells represent the cell population responsible for tumor initiation and progression. Resistance to cell death induced by cytotoxic agents is a characteristic shared by most identified cancer stem cells. In ovarian cancer, the CD44+/MyD88+ epithelial ovarian cancer (EOC) stem cells do not only represent the chemoresistant population, they are also able to repair the tumor and serve as tumor vascular progenitors. Targeting these cells is therefore necessary to improve treatment outcome. However, the previous demonstration that these cells are extremely chemoresistant, suggests that other forms of targeted therapy should be explored. We previously showed that the novel isoflavone derivative, NV-128, can induce caspase-independent cell death in ovarian cancer cells by inducing loss of mitochondrial membrane potential. We hypothesize that targeting mitochondrial bioenergetics may be a potent stimulus to induce cell death in the EOC stem cells. We demonstrate in this study that NV-128 is able to depress mitochondrial function leading to the activation of two independent pathways and cell death in these chemo-resistant cell population. Methods: A panel of CD44+/MyD88+ EOC stem cells was treated with NV-128 (1–10μg/ml). Inhibitory studies were done using the specific MEK inhibitor, U0126, or the ROS scavenger, MnTBAP. Mitochondrial integrity and function were assessed using Mitotracker Red, Mitotracker Green, MitoSox, and ApoSENSOR ADP/ATP kit. Cytoplasmic and mitochondrial fractions were prepared using the ApoAlertTM Cell Fractionation kit. Protein levels were determined using Western Blot. Results: NV-128 (10 μg/ml) significantly depressed mitochondrial function within 2h in all EOC stem cells tested. Treated cells had lower levels of ATP and Cox-IV, and higher levels of mitochondrial superoxide. Low cellular ATP led to mTOR inhibition through AMPKα1, while increased mitochondrial superoxide activated the mitochondrial MEK/ERK pathway and promoted Bax-dependent loss of mitochondrial membrane potential. Resulting cell death was characterized by Endo-G-induced but caspase-independent DNA fragmentation, as well as formation of autophagic vacuoles. Conclusion: We demonstrate that targeting the mitochondria in the EOC stem cells promotes a state of “cellular starvation” capable of activating two independent pathways: 1) AMPKα1 pathway leading to mTOR inhibition; and 2) mitochondrial MEK/ERK pathway leading to mitochondrial depolarization. The simultaneous activation of these pathways is a potent stimulus to induce cell death in cells. The demonstration that a compound can specifically target the mitochondria to induce cell death in this otherwise chemo-resistant cell population opens a new venue for treating ovarian cancer patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-221. doi:10.1158/1538-7445.AM2011-LB-221