Human papillomaviruses (HPV) are associated with a subset of head and neck squamous cell carcinoma (HNSCC), particularly HPV16. This study analyzed the presence and genotype of high risk HPVs, viral DNA load and transcription of the E6/E7 mRNAs, in 231 consecutive HNSCC. Twelve out of 30 HPV16 DNA-positive tumors displayed high E6/E7 mRNAs levels and were localized in the oropharyngeal region. While HPV-free and non-transcriptionally active HPV-related patients showed similar 5-years survival rates, E6/E7 expression was associated with a better prognosis. This emphasizes the importance of considering the transcriptional status of HPV-positive tumors for patient stratification. A gene expression profiling analysis of these different types of tumors was carried out. The most significant differentially expressed gene was CDKN2A, a known biomarker for HPVrelated cancer. Assessing both the expression level of the E6/E7 mRNAs and of CDKN2A in HNSCC is required to detect active HPV infection. Chromosomic alterations were investigated by Comparative Genomic Hybridation (CGH) analysis of tumors with transcriptionally active HPV and HPV-negative tumors. The loss of the chromosomal region 16q was found to be a major genetic event in HPV-positive lesions. A cluster of genes located in 16q21-24 displayed decreased expression levels, notably APP-BP1 that is involved in the modulation of the transcriptional activity of p53. In conclusion, this study highlights important criteria required to predict clinically active HPV infection, identifies new biological pathways implicated in HPV tumorigenesis and increases the understanding of HPV-HNSCC physiopathology that is required to develop new targets for therapy.Heavy consumption of tobacco and alcohol are the major risk factors for head and neck squamous cell carcinoma (HNSCC). However, recent epidemiological data indicate that high-risk human papillomavirus (HR-HPV), similar to those involved in cervical cancer onset and development, are associated with a subset of HNSCC 1 (for comprehensive review, see Refs. 2 and 3 and references therein). The anatomic site mostly associated with HPV infection in the upper aerodigestive tract is the oropharynx, especially the tonsils and tongue base. [4][5][6][7] The oncogenic potential of HPV involves the expression of the E6 and E7 viral oncoproteins, which disrupt the p53 and pRB signalling pathways, respectively. Typically, the absence of genetic or epigenetic alterations in the p53 and pRb pathways in HPV-positive cancer distinguishes them from HPV-negative disease.