Abstract Objectives; Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer types in the world. Despite of considerable advances in multimodality therapy, including surgery, radiotherapy and chemotherapy, the overall 5-year survival rate for patients with HNSCC is only 40% - 50%. Although a growing body of evidence indicates that long non-coding RNAs (lncRNAs) contribute to the initiation and development of various types of cancers, the role of lncRNA expression in human HNSCC remains unknown. In this study, we aimed to establish the onco-lncRNAome profiling of HNSCC from The Cancer Genome Atlas (TCGA) project. Materials and Methods; The Atlas of Noncoding RNAs in Cancer (TANRIC) database (http://ibl.mdanderson.org/tanric/_design/basic/index.html) was employed to retrieve the lncRNA expression information from the TCGA HNSCC RNA-sequencing data. Our recently generated RNA-sequencing data from 22 representative HNSCC cell lines (OPC-22 panel) were also included in this study. Bioinformatics approaches, such as differential gene expression analysis, survival analysis, principal component analysis, and Co-LncRNA enrichment analysis were performed. Results; Using TCGA HNSCC RNA-sequencing data from 426 HNSCC and 42 adjacent normal tissues, we identified 728 lncRNA transcripts significantly and differentially expressed in HSNCC. Among the 728 lncRNAs, 55 lncRNAs were significantly associated with cancer prognosis (overall survival and/or recurrence free survival). We also identified 140 lncRNA transcripts significantly and differentially expressed between Human Papilloma Virus (HPV) positive tumors and HPV negative tumors. 30 lncRNA transcripts were distinctly expressed between TP53 mutated tumors and TP53 wild type tumors. Among them, there were 19 overlapping genes up-modulated in HPV positive and TP53 wild type tumors. Co-LncRNA enrichment analysis suggested that protein-coding genes that are co-expressed with cancer-associated lncRNAs might be involved in malignant progression. Of interest, many differentially expressed lncRNAs in HNSCC were reflected in the HNSCC cell line panel. Conclusion; LncRNAs profiling could provide novel insights into the potential mechanisms of HNSCC oncogenesis. A unique set of lncRNAs may represent potential targets for diagnosis, therapy and prevention of HNSCC. Citation Format: Nijiro Nohata, Martin Abba, Panomwat Amornphimoltham, J. Silvio Gutkind. Comprehensive long non-coding RNA expression profiling from the TCGA HNSCC RNA-sequencing data. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1936.