This national online cross-sectional survey in Italy assessed primary care pediatricians' (PCPs) attitudes and practices regarding Human papillomavirus (HPV) vaccination and the contribution of several characteristics. The questionnaire was distributed from September 2016 to June 2017 to a random sample of 640 PCPs by email via an internet-link leading to a web-based survey platform (Lime Survey). Only 18.4% of PCPs always recommend the HPV vaccine to 11-12 year old boys. PCPs with longer practice activity, working in solo practice, always recommended the HPV vaccine to 11-12 year old girls, and believed that the vaccine was effective for boys were more likely to always recommend the HPV vaccine. PCPs working in a Region where the vaccination was actively recommended and provided free of charge to 11-12 year old boys had higher odds of recommending vaccination. More than two thirds of PCPs (77.4%) always recommend the HPV vaccine to 11-12 year old girls. PCPs who believed that the vaccine was effective for girls and safe in both boys and girls, who always talk with patients of 11-18 years or their parents about HPV infection and vaccination, and who obtain vaccine information from scientific journals were more likely to always recommend the vaccine. PCPs should employ evidence-based educational strategies in order to achieve a better coverage and to reduce the morbidities and mortality of diseases associated with HPV.