Abstract Carbonic anhydrase IX (CAIX) is a hypoxia and HIF-1 inducible protein that regulates intra- and extracellular pH under hypoxic conditions, and promotes tumor cell survival and invasion in hypoxic microenvironments. shRNA-mediated depletion of CAIX expression in mouse and human metastatic breast cancer cells, capable of inducing CAIX in hypoxia, resulted in regression of orthotopic mammary tumors and inhibition of spontaneous lung metastasis formation. CAIX depletion led to caspase-independent cell death and reversal of extracellular acidosis under hypoxic conditions in vitro. In addition, the CD44+/CD24-/low “cancer stem cell” compartment, which exhibited hallmarks of EMT (E-cadherin low/SMA high) was significantly enhanced in hypoxia, but was severely depleted in shRNA-CAIX knock-down cells as well as in cells treated with CAIX small molecule inhibitors. CAIX depletion or inhibition of its activity prevented mesenchymal conversion of the stem cells and also resulted in the suppression of expression of several EMT and “stemness” regulator genes. Treatment of mice harboring CAIX-positive 4T1 and MDA-MB-231/LM2 mammary tumors with novel CAIX-specific small molecule inhibitors that mimicked the effects of CAIX depletion in vitro resulted in significant inhibition of tumor growth and metastasis formation in both spontaneous and experimental models of metastasis, without any inhibitory effects on CAIX negative tumors, or any adverse toxic effects. This was associated with significant depletion of cells expressing “cancer stem cell” markers. Furthermore, interrogation of 3,630 human breast cancers revealed CAIX to be an independent poor prognostic biomarker for distant metastases and survival. Our findings demonstrate that CAIX is vital for the survival of “cancer stem cells” in hypoxic niches as well as for the growth and metastasis of hypoxic breast tumors. It is a specific, targetable biomarker for breast cancer metastasis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3305. doi:1538-7445.AM2012-3305