Background: Nuclear factor (erythroid-derived 2)-like 2 (NFE2L2) is a key transcription factor regulating oxidative stress. Activated NFE2L2 translocates to the nucleus and binds anti-oxidant response elements in the promoter regions of cytoprotective genes. It is negatively regulated by its protein complex partners, CUL3 and KEAP1. Recent HNSCC genome profiling studies identified NFE2L2, CUL3 and KEAP1 as recurrent somatically altered genes, suggesting an important role in HNSCC carcinogenesis. We hypothesized that germline variation in NFE2L2, CUL3 and KEAP1affects risk of HNSCC. Methods: The study population consisted of 751 cases (459 oral cavity, 292 oropharynx; 69% smoker) and 862 controls (50% smoker) from the University of Pittsburgh HNSCC case-control study. Subjects were genotyped for 22 single nucleotide polymorphisms (SNPs) located in or near NFE2L2 (10), CUL3 (8) and KEAP1(4) using Sequenom’s iPLEX assay. Odds ratios (OR) for HNSCC risk and corresponding 95% confidence intervals (CI) were calculated using logistic regression models. Additive and dominant genetic models were evaluated; common allele homozygotes were used as the reference group. All analyses were adjusted for age (continuous), sex (male, female), smoking status (never, ever) and alcohol use (never, ever). Results: Two SNPs in NFE2L2 (rs13001694, rs6726395) and two SNPS in CUL3 (rs1466723, rs3738952) were significantly associated with HNSCC risk in our study population (P< 0.05). The minor alleles of these SNPs were associated with increased risk of developing HNSCC (rs13001694, OR: 1.16, 95%CI: 1.00-1.35; rs6726395, OR: 1.17, 95%CI: 1.02-1.35; rs1466723, OR: 1.27, 95%CI: 1.03-1.56; and rs378952, OR: 1.54, 95%CI: 1.20-1.98). Conclusions: Our results suggest that germline variation in the NFE2L2/CUL3/KEAP1pathway affects risk of developing HNSCC. Improved understanding of the role of genetic variation in HNSCC carcinogenesis may aid the development of more effective, personalized prevention and diagnostic strategies.