Human papillomavirus (HPV) has been linked with development of oropharyngeal squamous cell carcinoma, a subset of head and neck cancer (HNC). This study aimed to evaluate the association between HPV infection and subsequent development of HNC and to report epidemiological information in Taiwan.This population-based cohort study retrieved patient data from the longitudinal health insurance database (LHID) of Taiwan's National Health Insurance Research Database (NHIRD) from 2005 to 2010 and analyzed it retrospectively. The crude incidence rate and incidence rate ratios with 95% confidence intervals of HNC were estimated in patients with and without HPV infection. A time-to-event analysis was conducted and multiple regression analysis was performed to identify factors associated with HNC in HPV-infected patients, including age at baseline, sex, and comorbidities.This study included the data of 25,520 HPV-infected and 1,061,817 noninfected patients. The HPV-infected group had a significantly higher proportion of females than the noninfected group (55.80% vs 50.66%, respectively; P < .0001). The incidence rate of HNC was 11.49 (males) and 5.83 (females) per 10 person-months versus 11.38 (males) and 3.90 (females) per 10 person-months in the infected and noninfected groups, respectively. HPV was significantly associated with cancer in females (hazard ratio = 1.520, 95% confidence interval 1.166-1.981), but not in males (hazard ratio = 1.000, 95% confidence interval 0.815-1.228). No significant differences were found in age between the HPV-infected and noninfected patients (49.20 ± 14.34 years vs 49.09 ± 13.82 years, respectively); and a slightly higher percentage of HPV-infected patients had a specific comorbidity than did noninfected patients 12.54% versus 9.43%, ischemic heart disease 14.22% versus 10.51%, hypertension 22.40% versus 19.54%, liver disease 22.88% versus 16.17%, and renal disease 7.14% versus 5.39%, respectively.Results of this study may help clinicians in the diagnosis, prognosis, and treatment of head and neck cancer.