Recent studies suggested that human papillomavirus (HPV) is an emerging risk factor of head and neck cancer (HNC), particularly for oropharyngeal cancer. Studies from the West showed a rising trend of HPV-related HNC despite a decrease of the overall HNC incidence. In contrast, the overall HNC incidence in Taiwan has continued to rise. It is not clear whether the incidence trends of HPV-related HNC in Taiwan have a similar pattern to those from countries with an overall decreasing incidence of HNC. This study examined the incidence trends of HPV-related and HPV-unrelated HNC in Taiwan using data from the Taiwan Cancer Registry. Our results showed that the incidence trends of HPV-related and HPV-unrelated HNC in Taiwan both rose during 1995-2009. The incidence of HPV-related HNC (1.3 per 100,000 in 1995 to 3.3 in 2009, annual percentage change (APC) 5 6.9, p < 0.0001) rose more rapidly than the incidence of HPV-unrelated HNC (10.4 per 100,000 in 1995 to 21.7 in 2009, APC 5 5.0, p < 0.0001). The rising trend of HPV-related HNC was particularly prominent for HNC occurring in tonsil (APC 5 8.2, p < 0.0001), in men (APC 5 7.5, p < 0.0001), and in those aged between 40 and 50 years (APC 5 8.5, p < 0.0001). Although the overall incidence of HNC in Taiwan has continued to increase, the most rapid rise is in the HPV-related HNC.