This study investigates the expression of hypoxia-inducible factor-l alpha (HIF-1α) and carbonic anhydrase IX (CAIX) in nasopharyngeal carcinoma (NPC) tissues and their correlation with clinicopathological features and prognosis in NPC patients. The expression of HIF-1α and CAIX proteins was detected by immunohistochemical staining in 129 samples of NPC and 20 samples of chronic nasopharyngitis. The correlations between the expression of these two proteins and clinicopathological features and prognosis were evaluated in NPC patients. Our results showed that the positive expression rates of HIF-1α and CAIX proteins in NPC were significantly higher than those in chronic nasopharyngitis (both P < 0.01). In addition, high HIF-1α protein expression was correlated with lymph node metastasis and advanced clinical stage for NPC patients (both P < 0.01), whereas there were no findings of correlations between CAIX protein expression and gender, age, T stage, node involvement and clinical stage (all P > 0.05). The Spearman analysis indicated that HIF-1α was positively correlated with CAIX expression (r = 0.249, P = 0.004). HIF-1α and CAIX co-expression was associated with the poor overall survival (OS), progression-free survival (PFS), loco-regional relapse-free survival (LRRFS) and distant metastasis-free survival (DMFS) in NPC patients (P = 0.017, P = 0.022, P = 0.033, and P = 0.017, respectively). Multivariate analysis showed that the positive expression of CAIX protein was an independent prognostic factor for PFS, LRRFS and DMFS. In conclusion, overexpression of HIF-1α and CAIX might be involved in the carcinogenesis and development of NPC and they were associated with patients' poor prognosis.