Lung cancer is the leading global cause of cancer-related mortality and is associated with poor prognosis. To improve survival rates of lung cancer patients, better understanding of tumorigenic mechanisms is necessary, which may lead to development of new therapeutic strategies. The hOGG1 and NTH1 genes act in the DNA BER repair pathway and their involvement in lung cancer pathogenesis has been analyzed in several populations. We analyzed targeted regions of the hOGG1 and NTH1 genes in 96 Brazilian patients with non-small-cell lung cancer (NSCLC) and 89 cancer-free, ethnically matched controls. The NTH1 c.98G>T polymorphism rs2302172 (p = 0.02 and p = 0.02 for allele and genotype frequency between cases and controls, respectively) and the 140-17C> T variant (rs2233518) (p = 0.02 and p = 0.02 for allele and genotype frequency between cases and controls, respectively) were detected in four lung cancer cases (4 %) while the NTH1 Q131K (C391A) polymorphism was found in seven lung cancer cases (7 %) (p = 0.001 and p = 0.008, for allele and genotype frequency between cases and controls, respectively). None of these sequence variants were detected in controls. The Ser326Cys (C1245G, rs1052133) polymorphism in the OGG1 gene was detected in 42 % of analyzed NSCLC patients and in 34 % of the controls (p = 0.11 and p = 0.25 for allele and genotype frequency between cases and controls, respectively). Our study provides preliminary evidence that polymorphisms in OGG1 do not contribute to development of NSCLC in Brazilian patients and that NTH1 polymorphisms may be associated with NSCLC pathogenesis.