Numerous reports have shown that the incidence for oropharyngeal cancer is increasing and that HPV is a risk factor. However, few studies have investigated the specific sub-sites of the oropharynx. Following our previous research on tonsillar cancer, we assessed the increase in incidence of base of tongue cancer and the prevalence of HPV in this disease. Between 1998 and 2007, 109 patients were diagnosed with base of tongue cancer in Stockholm County. 95 paraffin-embedded diagnostic tumor biopsies from patients were obtained and tested for HPV both by general HPV PCR and HPV-16/HPV-33 type-specific PCR. Expression of HPV-16 RNA was analyzed to confirm E6 and/or E7 expression. Incidence data were obtained from the Swedish Cancer Registry. An overall increase in the incidence of base of tongue cancer from 0.15/100,000 person years during 1970-1974 to 0.47/100,000 person years during 2005-2007 was found in Sweden. The prevalence of HPV in base of tongue cancer in Stockholm County increased from 58% during 1998-2001 to 84% during 2004-2007 (p