Triple negative breast cancer (TNBC) is defined phenotypically as the lack of ER, PR and HER2 expression, and comprises a heterogeneous group of breast cancers. Cancer stem cells (CSCs), identified as either ALDH1+ or CD44hi/CD24lo subpopulations in breast cancer, have been shown to be resistant to standard chemotherapy and associated with poor clinical outcome. In recent reports, the presence of ALDH1+ (but not ALDH1-) cells in axillary lymph nodes following neo-adjuvant chemotherapy was associated with poor overall survival. Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that orchestrates cell signaling through integrins and growth factor receptors. In addition to regulating the proliferation, survival, invasion and metastasis of cancer cells, FAK also plays a critical role in the self-renewal and survival of CSCs. VS-6063 (defactinib) is a potent, selective, and orally bioavailable FAK inhibitor with demonstrated tolerability and preliminary signs of clinical activity as a single agent and in combination with paclitaxel in phase I clinical trials. We report here that VS-6063 preferentially targets CSCs in preclinical models of TNBC. The effect of VS-6063 on CSCs was assessed in a panel of orthogonal assays. Treatment of human TNBC cells with VS-6063 in 3D matrigel reduced the percentage of Aldefluor+ CSCs, Hoechst dye-excluding side population (SP) CSCs, and tumorsphere-forming efficiency in a serial tumorsphere passaging assay, suggesting that VS-6063 preferentially inhibits CSCs. VS-6063 also reduced the proportion of Aldefluor+ CSCs in primary breast cancer tissue specimens cultured ex vivo. Consistent with the concept that the effect of VS-6063 on CSCs is mediated by FAK inhibition, siRNA-mediated knockdown of FAK in SUM159 TNBC cells recapitulated the inhibitory effect of VS-6063 on CSCs. In contrast, the standard-of-care (SoC) chemotherapeutic agents paclitaxel and doxorubicin enriched the percentage of CSCs, suggesting that these SoC agents preferentially target bulk tumor cells relative to CSCs. When administered in combination, VS-6063 attenuated the chemotherapy-induced enrichment of CSCs. Following oral administration of VS-6063 in the MDA-MB-231 human TNBC xenograft model in vivo, reduction of CSCs in tumors was evidenced by a decrease in secondary tumorsphere-forming efficiency. Importantly, cells dissociated from VS-6063-treated tumors displayed reduced tumor-initiating capability upon re-implantation into immunodeficient mice in limiting dilutions. In summary, our results indicate that the FAK inhibitor VS-6063 preferentially targets TNBC CSCs and support the clinical development of VS-6063 in combination with SoC agents, such as paclitaxel, to potentially improve clinical outcomes for patients with TNBC through simultaneous targeting of both CSCs and bulk tumor cells. Citation Format: Qunli Xu, Vihren N. Kolev, Quentin G. Wright, Jennifer E. Ring, Christian M. Vidal, Irina M. Shapiro, David T. Weaver, Mahesh V. Padval, Jonathan A. Pachter. Focal adhesion kinase (FAK) inhibitor VS-6063 (defactinib) preferentially targets cancer stem cells in triple negative breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3908. doi:10.1158/1538-7445.AM2014-3908