Identification of new nasopharyngeal carcinoma (NPC) biomarkers is of great clinical value for the diagnosis and treatment of NPC.HOTAIR, a cancer-related long non-coding RNA, was tested and its prognostic value for NPC was evaluated. As determined usingin situhybridization (ISH), 91 of 160 (56.87%) paraffin-embedded NPC biopsies showed high expression levels ofHOTAIR(staining index score ≥ 6).HOTAIRwas upregulated in tumors with a large size (P= 0.021), more advanced clinical stage (P= 0.012) and increased lymph node tumor burden (P= 0.005). Quantified using real-time PCR, HOTAIRexpression levels in fresh tissue and paraffin-embedded samples were 5.2 ˜ 48.4-fold higher compared with non-cancer tissue samples. Moreover,HOTAIRexpression levels increased with clinical stage progression, which was consistent with ISH findings in the paraffin-embedded tissue. Most importantly, NPC patients with higherHOTAIRlevels had a poor prognosis for overall survival using univariate and multivariate analysis. In addition,HOTAIRmediated the migration, invasion and proliferation of NPC cellsin vitro.HOTAIRis a potential biomarker for the prognosis of NPC, and dysregulation ofHOTAIRmight play an important role in NPC progression.