To examine the prognostic value of hypoxia inducible factor HIF-1a, CA-IX, and OPN on clinical outcome in patients with T1-T2 supraglottic laryngeal squamous cell carcinoma (LSCC) treated with primarily radiotherapy (RT). Retrospective cohort study. Tumor tissue sections of 60 patients with T1-T2 supraglottic LSCC treated with primarily radiotherapy were assessed immunohistochemically for expression of HIF-1a, CA-IX, and OPN. The relationship of protein expression and classical clinical parameters with clinical outcome was studied, using Cox regression and Kaplan-Meier survival analyses. Neither HIF-1a nor CA-IX was of prognostic significance toward local control or overall survival in T1-T2 supraglottic LSCC. Cox regression survival analysis showed no relation between HIF-1a or CA-IX expression and local control (HR [hazard ratio] 1.07, CI [95% confidence interval] 0.29-3.87; HR 0.34, CI 0.04-2.58). Furthermore, OPN expression was not associated with local control (HR 1.37, CI 0.45-4.17) and overall survival (HR 0.99, CI 0.44-2.21). Our earlier findings in T1-T2 glottic LSCC (Schrijvers et al., 2008) could not be confirmed. The absence of prognostic significance for HIF-1a and CA-IX toward local control in supraglottic LSCC, unlike glottic LSCC, suggests that supraglottic LSCC might represent another biological entity.