Human papillomavirus (HPV) has been recently recognised as a carcinogenic factor for a subset of head and neck cancers (HNC). In Europe, France has one of the highest incidence rates of HNC. The aim of this study is to explore changes in HNC incidence in France, potentially in relation with infection by HPV. HNC were classified into two anatomical groups: potentially HPV-related and HPV-unrelated. Trends over the period 1980-2012 were analysed by an age-period-cohort model based on data from eleven French cancer registries. Among men, the age-standardised incidence rate (ASR) of HNC decreased in both groups, but less so for HPV-related sites as compared to unrelated sites, especially in recent years (annual percentage change [APC] over the period 2005-2012: -3.5% vs. -5.4%). Among women, the ASR increased in both groups, but more rapidly for HPV-related as compared to unrelated sites (APC over the period 2005-2012: +1.9% vs. -0.4%). This preferential growth of HPV-related versus unrelated HNC was observed in the cohorts born from 1930 to 1935. The differences in trends between possible HPV-related and HPV-unrelated sites suggest an increasing incidence of HNC due to HPV infection. The difference was less marked in men as compared to women, most likely because of a higher contamination in the HPV-related group by cancers due to tobacco or alcohol consumption. The pattern observed is consistent with observations made in other countries, with studies of HPV prevalence in HNC and the evolution of sexual behaviour in France.