Human papillomavirus (HPV) vaccines protect against infections with the most oncogenic HPV types, cervical intraepithelial neoplasia (CIN) and cervical cancer. We investigated whether development of cervical intraepithelial neoplasia (CIN) lesions in HPV-vaccinated women is associated with vaccine-targeted HPV types or not. Linkage of the Swedish vaccination and cervical screening registries identified all females born 1980-2000 who had been HPV vaccinated before December 31, 2014 (n = 305,320) and had attended cervical screening in 2006-2018 (n = 79,491). We further selected women HPV vaccinated below 17 years of age and screened in the capital region (n = 5,874). Among those, 125 developed CIN and had a cervical cryopreserved sample available (42.5% of all eligible CIN cases). After 1:2 matching to disease-free HPV vaccinated controls (n = 242), samples were analyzed for HPV DNA and associations between HPV type and CIN diagnosis were estimated with conditional logistic regression. Vaccine-targeted HPV types were rare among both CIN cases (2.4% HPV16, 0.8% HPV18) and their matched controls (0.4% HPV16 and 18). No woman had HPV6 or 11. The CIN lesions were associated with the nonvaccine HPV types 31, 33, 42, 45, 51, 52, 56, 59 and 66. CIN lesions among young HPV vaccinated women are mostly attributable to infection with nonvaccine HPV types. The phenomenon may be important for surveillance and design of cervical cancer control strategies.