Journal Article ; Approximately 1-9 % of all head and neck squamous cell carcinomas are neck metastases from clinically undetectable primary tumors. Human papillomavirus (HPV) and Epstein-Barr virus (EBV) are proven carcinogenic factors that are associated with oropharyngeal squamous cell carcinoma and nasopharyngeal carcinoma, respectively. In the present study, we evaluated the prevalence of these viruses in neck metastases from unknown primary squamous cell carcinoma.We evaluated fresh samples from a consecutive series of 22 neck dissections for metastases from unknown primary squamous cell carcinoma obtained between 2010 and 2012 at a single institution. The samples were tested for the presence of HPV E6 and E7 mRNA and EBV DNA.Oncogenic viral infections were detected in 12 cases (54 % total; 2 HPV18, 5 HPV16, 2 EBV infection, and 3 EBV/HPV16 coinfections). The most frequent primarily involved neck level in our series was IIA (70 %), which had the highest prevalence of viral infection (66 %). We did not find any other significant correlations between virus detection and clinicopathologic parameters or prognosis.Neck metastasis from unknown primary squamous cell carcinoma could be another virus-related malignancy in the head and neck region, along with nasopharyngeal and oropharyngeal carcinoma. An evaluation of the impact of viral infection on patient prognosis and sensitivities to different treatment modalities could modify our prognostic assessments and treatment planning. Furthermore, virus detection would have a decisive impact on diagnostic/decisional algorithms, especially if detection methods are implemented on cytologic samples (e.g., thin prep).