Carbonic anhydrase 9 (CA9), which regulates cellular proliferation and the acid-base balance, is known as prognostic factor in various types of cancer. The aim of this study is to investigate the clinical implications of CA9 expression in patients with hepatocellular carcinoma. Immunohistochemical staining for CA9 was performed on tissue microarrays of hepatocellular carcinoma and paired non-neoplastic liver tissue from a training cohort of 838 patients and a validation cohort of 225 patients. Membranous staining in more than 5 % of the tumor cells was considered to indicate CA9 positivity. The prognostic value of CA9 expression was statistically evaluated. In the training cohort, CA9 positivity (181 cases, 21.5 %) was significantly correlated with shorter overall survival (OS; p < 0.001) and recurrence-free survival (RFS; p = 0.004). In multivariate analysis, CA9 positivity was independently associated with reduced OS (p = 0.023), but not significantly associated with RFS (p = 0.384). These results were validated in an additional cohort (CA9 positivity in 35 cases, 15.6 %; OS, p = 0.015; RFS, p = 0.979). Pooled cohort analysis showed that this predictor was independently associated with higher mortality (OS; p < 0.001). These data indicate that CA9 expression is a poor prognostic factor in resectable hepatocellular carcinoma (HCC) patients.