Abstract DNA from i) fresh tissues derived out of 89 women with CaCx (61 HPV16/18 positive) and ii) cervical scrapes from 213 cytologically normal women (73 HPV16/18 positive) were genotyped for HLA DQB1*03 by PCR and RFLP. The distribution of the genotypes of HLA DQB1*03 differed significantly between the malignant and control subjects (p= 0.022). The homozygous genotype was overrepresented among those having CaCx (ORage-adjusted=2.94, 95% CI= 1.49-5.81, p=0.002), or HPV16/18 positive CaCx (ORage-adjusted =2.32, 95% CI= 1.07-5.01; p=0.033), when this was compared to the other genotypes (HLADQB1*03 non-homozygous, i.e. heterozygous and null together). Analysis restricted to the HPV16/18 positive CaCx and cytologically normal subjects failed to show such association. The heterozygous genotype, instead, showed a negative association with HPV16/18 positive CaCx over the null genotype (ORage-adjusted =0.42, 95% CI= 0.18-0.96; p=0.040) when HPV16/18 positive CaCx cases were compared with HPV negative cytologically normal controls. The association of HLA DQB1*03 homozygosity with CaCx was noted among those of age < 47 years. The genotypes of HLA DQB1*03 are likely to be important in determining the susceptibility to HPV or HPV16/18 related CaCx in Indian women.