Carbonic anhydrase IX (CA IX) is a unique member of the CA gene family. In contrast to the other isozymes, it has been implicated in regulation of cell proliferation, adhesion, and malignant cell invasion. In a recently described knockout mouse model for CA IX deficiency, the only phenotypic abnormalities were limited to the gastric mucosa, while no changes were observed in the other tissues known to express CA IX in rats and humans. Here we investigated the expression of CA IX mRNA and protein in mouse tissues. Immunohistochemical (IHC) analysis showed strong staining in the gastric mucosa. Moderate reactions were seen in the colon enterocytes and pancreatic acini. The expression pattern of CA IX was similar in certain human and rodent tissues, although some differences existed, especially in the gut epithelium. Reverse transcriptase PCR analyses surprisingly revealed strong signals for CA IX mRNA in the kidney and skeletal muscle, while the IHC and Western blotting showed no or weak signals for the corresponding protein. This result suggests a tight tissue-specific post-transcriptional control for CA IX expression, possibly related to the physiological demands.