Polymorphisms at N-acetyl transferase 2 locus (NAT2) lead to slow, intermediate and rapid acetylation properties of the enzyme. Improper acetylation of heterocyclic and aromatic amines, present in tobacco, might cause DNA adduct formation. Generally, DNA repair enzymes remove these adduct to escape malignancy. But, tobacco users carrying susceptible NAT2 and DNA repair loci might be at risk of oral leukoplakia and cancer. In this study, 389 controls, 224 leukoplakia and 310 cancer patients were genotyped at 5 polymorphic sites on NAT2 and 3 polymorphic sites on each of XRCC1 and XPD loci by PCR-RFLP method to determine the risk of the diseases. None of the SNPs on these loci independently could modify the risk of the diseases in overall population but variant genotype (Gln/Gln) at codon 399 on XRCC1 and major genotype (Lys/Lys) at codon 751 on XPD were associated with increased risk of leukoplakia and cancer among slow acetylators, respectively (OR 5 4.2, 95% CI 5 1.2-15.0; OR 5 1.6, 95% CI 5 1.1-2.3, respectively). Variant genotype (Asn/Asn) at codon 312 on XPD was also associated with increased risk of cancer among rapid and intermediate acetylators (OR 5 1.9, 95% CI 5 1.2-2.9). Variant C-G-A haplotype at XRCC1 was associated with increased risk of leukoplakia (OR 5 1.7, 95% CI 5 1.2-2.4) but leukoplakia and cancer in mixed tobacco users (OR 5 3.1, 95% CI 5 1.4-7.1, OR 5 2.4, 95% CI 5 1.1-5.4, respectively) among slow acetylators. Although none of the 3 loci could modulate the risk of the diseases independently but 2 loci in combination, working in 2 different biochemical pathways, could do so in these patient populations. ' 2007 Wiley-Liss, Inc.Key words: tobacco use; oral cancer; leukoplakia, NAT2; XPD; XRCC1; polymorphism As an early sign of damage to oral mucosa, tobacco smokers and chewers often develop different precancerous lesions, such as leukoplakia, erythroplakia, submucous fibrosis, etc., and these lesions are easily accessible to diagnosis. Annual incidence of oral leukoplakia has been reported as 0.2-11.7% in different populations of India 1-3 and about 2-12% of leukoplakia becomes malignant within several years. 2 Since leukoplakia is one of the good predictors of oral cancer so diagnosis and treatment of leukoplakia will be a useful strategy to control oral cancer incidence. Annually about 270,000 cases of oral cancer are reported worldwide but about 82,000 of them are diagnosed in India. 4 Major procarcinogens present in the tobacco smoke are polycyclic aromatic hydrocarbons, aromatic and heterocyclic amines and nitroso-compounds whereas nitrosamines and aromatic and heterocyclic amines are major components present in smokeless tobacco. Most of the tobacco carcinogens generally undergo bioactivation and inactivation by phase I and phase II enzymes respectively. Human N-acetylation transferase 2 (NAT2) is one of the phase II enzymes that participate in the bioconversion of aromatic and heterocyclic amines and variation in NAT2 enzyme activity is defined as polymorphism in N-acetylation capacit...