Cells of the growing tumor tissue are exposed to physiological stresses connected with insufficient delivery of oxygen (hypoxia) and accumulation of acidic products of the glycolytic metabolism (acidosis). Adaptation to these microenvironmental stresses involves remodeling of the cellular expression program mediated by hypoxia-inducible factor (HIF), which activates broad array of genes functionally involved in angiogenesis, anaerobic glycolysis, de-adhesion, invasion etc. This leads to increased aggressiveness of tumors, metastatic spread and poor response to therapy. Genes coding for transmembrane carbonic anhydrase (CA) isoforms IX and XII are induced in response to low oxygen as a part of the hypoxic transcriptome. Moreover, CA IX is a direct target of HIF and serves as a surrogate marker of hypoxia and prognostic indicator. Its expression is strongly linked to different types of tumors with the HIF pathway activated due to genetic defect or physiological hypoxia. CA IX (and possibly also CA XII) is participates in pH regulation, which is important for survival of hypoxic cells. Both enzymes are therefore promising therapeutic molecules targetable by inhibitors of CA activity. Some of these sulfonamide compounds and their derivatives are capable to block CA-mediated pH regulation in hypoxia. This review summarizes research data related to distribution, regulation and functional aspects of CA IX and CA XII, and describes emerging possibilities for clinical exploitation of CA inhibitors as imaging tools and anticancer drugs.