Hypoxia is a consistent finding in fast-growing tumors; it contributes to tumor progression and therapeutic responses. We explored the expression of hypoxia-associated biomarkers in head and neck squamous cell carcinoma (HNSCC) to assess their relationship with clinical factors in HNSCC. In total, 90 patients with HNSCC were enrolled. Expression of HIF-1α, HSP70, HSP90, VEGF, IGF-1R, and P16 was investigated by immunohistochemistry. Their correlations with clinical factors, including location of primary sites, T stage, N stage, M stage, HPV status, primary treatment success/failure, recurrences, disease-free survival (DFS), and overall survival, were analyzed. HIF-1α, HPS70, HPS90, VEGF, and IGF-1R were positive in 33 of 89 (37.1 %), 62 of 87 (71.3 %), 83 of 89 (93.3 %), 41 of 87 (47.1 %), and 50 of 56 (89.3 %) cases, respectively. Expression levels of some of these markers were correlated. High HIF-1α or HSP 70 correlated with poor DFS, and expression of HSP70 correlated with LN metastasis. HPV-related carcinomas showed high HSP 70 and IGF-1R expression. Hypoxia-associated proteins were highly expressed and associated with aggressive clinical features in HNSCC. Expression of HIF-1α or HSP70 can be considered poor prognostic indicator in HNSCC. Our results suggest that hypoxic signaling is activated in HNSCC, especially in HPV-related tumors.