Background The new nine-valent human papillomavirus (HPV) vaccines includes the four HPV genotypes (6, 11, 16 and 18) targeted by the quadrivalent HPV vaccine, plus five additional oncogenic types (31, 33, 45, 52, and 58), and potentially increases the overall prevention of cervical cancer. Objective To determine the prevalence of high-risk viral genotypes according to the protection offered by the actual HPV vaccines, and their association and potential impact on the incidence of high-grade lesions. Methods Cross-sectional study. A total of 595 consecutive women in whom HPV infection had been detected in a cervical smear during routine gynaecological health checks were included. Smear results were classified using the Bethesda system. HPV genotyping was performed using Linear Array HPV genotyping test and they were classified according to the International Agency for Research on Cancer assessment of the carcinogenicity of different HPV types. Odds ratios (OR) with their 95% confidence intervals (95% CI) were estimated by logistic regression, adjusting for age and immigrant status. Prevented fraction among the exposed (PFe-adjusted) was determined as a measure of impact. Results At least one of the additional five high-risk HPV genotypes present in the nine-valent HPV vaccine was detected in 37.66% of women. After excluding women with genotype 16 and/or 18 co-infection, high-risk genotypes (31, 33, 45, 52, 58) were associated with a higher risk of intraepithelial lesion or malignancy: adjusted OR: 3.51 (95% CI: 1.29–9.56), PFe-adjusted 0.72 (95% CI: 0.22–0.90). Genotypes that are still non-vaccine-targeted were detected in 17.98% of women, and non-significantly associated with high-risk lesions. Conclusion The greater protection of the nine-valent HPV vaccine is likely to have impact, because in the absence of genotype 16 or 18 infection, these five genotypes on their own would multiply the risk of a high-grade lesion by 3.5-fold and would be responsible for 72% of high-grade lesions.