Several recent studies have reported different associations between HLA specificities and human papillomavirus (HPV)-associated disease of the cervix. We report the distribution of DQA1 and DQB1 genes and HPV infection in a population-based case-control study including 92 patients with histologically verified cervical intraepithelial neoplasia grade II-III (CIN II-III) (thus including moderate and severe dysplasia and carcinoma in situ) and 225 control subjects. We found an overrepresentation of the DQA1*0102-DQB1*0602 haplotype among HPV-positive cases compared with controls. The association was even stronger when comparing HPV-16-positive cases with HPV-16-positive controls. In addition, among HPV-16-positive individuals, we observed a decreased frequency of DQA1*0102-DQB1*0604 in cases compared with controls. We were not able to detect any association between CIN II-III and DQB1*03. Compared with previous findings in cervical cancer, our data indicate that carrying the DQA1*0102-DQB1*0602 haplotype gives an increased risk of developing CIN when infected with HPV-16, without influencing progression to cancer.