Head and neck squamous cell carcinoma (HNSCC) is malignancy which impairs the life quality of patients and seriously threatens human life. HPV infection has increasingly been recognized as a significant etiology for HNSCC initiation and progression. Emerging evidences have suggested that HPV+and HPV- HNSCC patients showed different responses to cancer therapy, which may be attributed to varied immune cell infiltration in tumor microenvironment. In the present study, we made a comprehensive analysis of significant genes and immune cell infiltration in HNSCC with different HPV status. Firstly, transcriptome data of HNSCC samples with available HPV status was downloaded from The Gene Expression Omnibus (GEO) database and differential expression analysis was performed. A total of 61 differentially expressed genes (DEGs) including 32 upregulated and 29 downregulated genes were identified in HPV+ HNSCC when compared to HPV- HNSCC. Further enrichment analysis demonstrated these DEGs were closely associated with cancer-related biological functions and signaling pathways. Infiltration of 22 kinds of immune cells was evaluated by CIBERSORT based on gene expression matrix. As a result, it was indicated that the infiltration of follicular helper T cells, gamma delta T cells, monocytes, eosinophils and neutrophils presented significantly differences between HPV+ and HPV- HNSCC. Collectively, our findings may provide new evidences for the development of immunotherapy and personalized precision medicine for HNSCC with different HPV status.Copyright © 2020 Elsevier B.V. All rights reserved.