The expression levels of hypoxia-inducible factor 1alpha(HIF-1α) and HIF-2α in pancreatic cancer(PC) and their association with clinicopathologic characteristics were investigated in order to elucidate their roles in the development of PC. HIF-1α and HIF-2α m RNA levels in 20 patients with PC were detected by quantitative real-time polymerase chain reaction. The expression of HIF-1α and HIF-2α protein in samples from other 90 patients with PC was measured by immunohistochemistry. Correlations between the expression of HIF-1α or HIF-2α and clinicopathologica features and prognosis were analyzed. The expression of both HIF-1α and HIF-2α m RNA was up-regulated in most cancer tissues(P<0.05). HIF-1α staining was weakly positive in most cancer tissues and strongly positive in adjacent pancreas tissues(P<0.05). Clinicopathologic analysis revealed that relatively strong HIF-1α expression in cancer tissues was related to greater invasion(P<0.05), higher tumor pathologic stage(P<0.05), higher American Joint Committee on Cancer(AJCC) stage(P<0.05) and shorter overall survival time(P<0.05). Conversely, HIF-2α staining was strongly positive in most cancer tissues and weakly positive in adjacent pancreas tissues. Clinicopathologic analysis revealed that relatively strong HIF-2α expression in cancer tissues was related to less invasion(P<0.05), lower tumor pathologic stage(P<0.05), lower AJCC stage(P<0.05) and longer overall survival time(P<0.05). Moreover, the HIF-1αhigh/HIF-2αlow group showed a shorter survival time than the HIF-1αlow/HIF-2αhigh group. In conclusion, although HIF-1α and HIF-2α m RNA expression patterns are the same, their protein expression patterns are significantly different and they play different roles in PC. Combined analysis of HIF-1α and HIF-2α expression might be useful to predict the prognosis of patients with PC. The expression levels of hypoxia-inducible factor 1alpha (HIF-1α) and HIF-2α in pancreatic cancer (PC) and their association with clinicopathologic characteristics were investigated in order to elucidate their roles in the development of PC. HIF-1α and HIF- 2α m RNA levels in 20 patients with PC were detected by quantitative real-time polymerase chain reaction. The expression of HIF-1α and HIF-2α protein in samples from other 90 patients with PC was measured by immunohistochemistry. Correlations between the expression of HIF 1α or HIF-2α and clinicopathologica features and prognosis were analyzed. The expression of both HIF-1α and HIF-2α m RNA was up-regulated in most cancer tissues (P <0.05). HIF-1α staining was weakly positive in most cancer tissues and strongly positive in adjacent pancreas tissues (P <0.05). Clinicopathologic analysis revealed that relatively strong HIF-1α expression in cancer tissues was related to greater invasion (P <0.05), higher tumor pathologic stage (P <0.05) and shorter overall survival time (P <0.05) .Conversely, HIF-2α staining was strongly positive in most cancer tissues and weakly positive in adjacent pancreas tissues. Clinicopathologic analysis revealed that relatively strong HIF-2α expression in cancer tissues was related to less invasion (P <0.05), lower tumor pathologic stage (P <0.05), lower AJCC stage (P < 0.05) .In addition, the HIF-1αhigh / HIF-2αlow group showed a shorter survival time than the HIF-1αlow / HIF-2αhigh group. In conclusion, although HIF- protein expression patterns are significantly different and they play different roles in PC. Combined analysis of HIF-1α and HIF-2α expression might be useful to predict the prognosis of patients with PC.