Sexually transmitted infection with the human papillomavirus (HPV) is responsible for a significant burden of human cancers involving the cervix, anogenital tract, and oropharynx. Studies in the United States and Europe have demonstrated an alarming increase in the frequency of HPV-positive oropharyngeal cancer, but the same direct evidence does not exist in Canada. Using the London Health Sciences Centre pathology database, we identified tonsillar cancers diagnosed between 1993 and 2011. Real-time polymerase chain reaction was then used on pre-treatment primary-site biopsy samples to test for DNA from the high-risk HPV types 16 and 18. The study cohort was divided into three time periods: 1993–1999, 2000–2005, and 2006–2011. Of 160 tumour samples identified, 91 (57%) were positive for HPV 16. The total number of tonsillar cancers significantly increased from 1993–1999 to 2006–2011 (32 vs. 68), and the proportion of cases that were HPV-positive substantially increased (25% vs. 62%, p< 0.002). Those changes were associated with a marked improvement in 5-year overall survival (39% in 1993–1999 vs. 84% in 2006–2011, p< 0.001). When all factors were included in a multivariable model, only HPV status predicted treatment outcome. The present study is the first to provide direct evidence that HPV-related oropharyngeal cancer is increasing in incidence in a Canadian population. Given the long lag time between HPV infection and clinically apparent malignancy, oropharyngeal cancer will be a significant clinical problem for the foreseeable future despite vaccination efforts.