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Background: Carbonic anhydrase IX (CAIX) is an enzyme upregulated by hypoxia during tumour development and progression. This study was conducted to assess if the expression of CAIX in tumour tissue and/or plasma can be a prognostic factor in patients with non-small cell lung cancer (NSCLC). Methods: Tissue microarrays containing 555 NSCLC tissue samples were generated for quantification of CAIX expression. The plasma level of CAIX was determined by ELISA in 209 of these NSCLC patients and in 58 healthy individuals. The CAIX tissue immunostaining and plasma levels were correlated with clinicopathological factors and patient outcome. Results: CAIX tissue overexpression correlated with shorter overall survival (OS) ( P =0.05) and disease-specific survival (DSS) of patients ( P =0.002). The CAIX plasma level was significantly higher in patients with NSCLC than in healthy individuals ( P <0.001). A high level of CAIX in the plasma of patients was associated with shorter OS ( P <0.001) and DSS ( P <0.001), mostly in early stage I+II NSCLC. Multivariate Cox analyses revealed that high CAIX tissue expression ( P =0.002) was a factor of poor prognosis in patients with resectable NSCLC. In addition, a high CAIX plasma level was an independent variable predicting poor OS ( P <0.001) in patients with NSCLC. Conclusion: High expression of CAIX in tumour tissue is a predictor of worse survival, and a high CAIX plasma level is an independent prognostic biomarker in patients with NSCLC, in particular in early-stage I+II carcinomas.