Background: Patients with hypopharyngeal cancer have a 5-year survival of only 15-30%. Human papillomavirus (HPV) is a risk factor and a favorable prognostic factor for oropharyngeal carcinoma, and p16 has been suggested as a surrogate marker for HPV-induced cancer. However, few studies have been performed on HPV and p16 in hypopharyngeal cancer. Methods: 109 pretreatment hypopharyngeal cancer biopsies were analyzed for presence of HPV and p16 overexpression, and the results were correlated to patient survival. Results: Out of 109 tumors 7 were HPV-positive (4 HPV16) and 18 overexpressed p16. There was some correlation between survival and HPV status, but not with regard to p16 expression. Notably, all patients with HPV16 positive tumors, also overexpressing p16, lived tumor free for more than 3 years. Conclusions: Our results indicate that HPV-induced hypopharyngeal cancer is rare and that p16 is not a suitable biomarker for presence of HPV in this tumor type. © 2013 Wiley Periodicals, Inc. Head Neck, 2013.