Vaccines against human papillomaviruses are covered by statutory health insurances in Germany since March 2007. A reduction of cervical and other HPV-associated cancers is expected. Incidence rates of HPV-associated cancers preceding the introduction of vaccines are unknown. These, however, are important for assessing the effects of HPV vaccines. The aim of the present study was to bridge this knowledge gap. Based on cancer registry data from seven federal states, average yearly incidence rates for cervical, anogenital, oropharyngeal cancers and cancers of the oral cavity were calculated for the period 2003 to 2007. Additionally, estimated numbers of cases give an overview on the total burden of disease caused by HPV-associated cancers in Germany. Incidence trends from 2003 to 2013 are also presented. In Germany, 11,686 cases of invasive HPV-associated cancers occurred yearly before the introduction of HPV vaccines. The most common sites are cervical cancers for women (4,387 cases) and oropharyngeal cancers for men (2,770 cases) with age-standardized incidence rates of 8.8 and 5.9 cases per 100,000 persons, respectively. The age-standardized incidence rate for in situ cervical cancers amounts to 23.5 cases per 100 000 women. Incidence trends show significant increases of invasive vulvar, penile and anorectal cancers. This work presents robust incidence data of HPV-associated cancers in Germany prior to the introduction of the HPV vaccine. Effects of HPV vaccines on the incidence of HPV-associated cancers can be estimated for Germany earliest in 2019.