HPV-vaccinated women develop CIN III very rarely. We have identified a study group of 38 such patients and showed that a specific HPV genotype prevalence in those cases equals the prevalence of HPV genotypes in CIN III present in the general Czech population. In all cases, CIN III was diagnosed within 3 years after having completed the HPV vaccination. We conclude that dysplasia was present before the vaccination in those women. A history of abnormal pre-vaccination PAP smear result (present in 78 % of women in the study group) and age of over 17 by the time of vaccination completion (97 % of women in the study group) are identified as probable factors increasing the risk of CIN III development after HPV vaccination.