Human leukocyte antigens (HLAs) present foreign antigens to the immune system and may be important determinants of cervical neoplasia. Previously published associations between HLA and cervical neoplasia exhibit considerable variation in findings. The biomarkers of cervical cancer risk (BCCR) case-control study addressed the role of specific HLA alleles as cofactors in the development of high-grade cervical intraepithelial neoplasia (HG-CIN) based on the most consistent evidence from published literature. Cases (N 5 381) were women with histologically-confirmed HG-CIN attending colposcopy clinics and controls (N 5 884) were women from outpatient clinics with normal cytological screening smears. Subjects were mainly of French-Canadian descent. Cervical specimens were tested for human papillomavirus (HPV) DNA and HLA genotypes by PGMY L1 consensus primer PCR and a PCR sequence-specific primer method, respectively. Unlike other studies, the DQB1*03 and DRB1*13 allele groups were not associated with risk of HG-CIN. The B7-DRB1*1501-DQB1*0602 haplotype was associated with a 41% overall reduction in HG-CIN risk (odds ratio [OR] 5 0.59; 95% confidence interval [CI]: 0.36-0.96), and an 83% reduction in risk of HG-CIN among HPV 16 or HPV 18-positive subjects (OR 5 0.17; 95%CI: 0.05-0.54). Paradoxically, however, the same haplotype was associated with HPV 16/18 infection risk among controls (OR 5 8.44, 95%CI: 1.12-63.73). In conclusion, the B7-DRB1*1501-DQB1*0602 haplotype was protective against HG-CIN, especially in individuals infected with oncogenic HPV, but the mechanism of the association seems to involve multiple steps in the natural history of HPV and CIN. ' 2008 Wiley-Liss, Inc.Key words: cervical intraepithelial neoplasia; human leukocyte antigen; human papillomavirus; case-control study After breast cancer, cervical cancer is the second most common cancer in women worldwide, with 493,000 new cases and over 273,000 deaths annually. 1 It is well established that the cervical infection caused by one of up to 18 oncogenic human papillomaviruses (HPV) is the main causal factor in cervical cancer, with HPV 16 alone accounting for over half of all cases. 2 In fact, HPV infection can be considered a necessary intermediate step in cervical carcinogenesis. 3 On the other hand, despite the presence of asymptomatic cervical HPV infection in 5-50% of women of reproductive age, 4,5 only a small fraction of infected women will develop cervical cancer. Thus, HPV infection alone is not a sufficient cause of cervical cancer, which underscores the need to identify cofactors that may mediate risk of persistent HPV infection or progression to cervical dysplastic changes and overt neoplasia. The human leukocyte antigens (HLA) mediate the presentation of HPV antigens to the immune system and thus may either predispose to or protect against development of HPV-associated cervical neoplasia. 6 Previous case-control studies examining the relationship have suggested that certain HLA polymorphisms are associated with risk of neoplastic tran...