Cigarette smoking is a major risk factor for squamous cell carcinoma of the head and neck (SCCHN), but only a fraction of those exposed to cigarette smoke develops SCCHN, suggesting variation in individual susceptibility. Tobacco smoke contains a number of carcinogens that cause various kinds of damage to DNA. In this study, we simultaneously measured benzo [a]pyrene diol epoxideinduced DNA damage and chromosomal aberrations by the comet assay and the mutagen sensitivity assay, respectively, in cultured primary lymphocytes from newly recruited 123 patients with SCCHN and 136 age-and sex-matched controls. Using the control median as the cut-off, the elevated risk of SCCHN was 2.35 (95% CI, 1.37-4.03), 2.28 (95% CI, 1.34-3.98) and 3.25 (95% CI, 1.85-5.07) for high levels of tail extension, tail length and oliver tail moment of the comet assay, respectively, and 1.75 (95% CI, 1.04-2.94) for high levels of chromosomal aberrations of the mutagen sensitivity assay. The effects of these 2 types of measurements were additive; subjects with high levels of both DNA damage and chromosomal aberrations had a 4.77-fold increased risk (95% CI, 2.73-8.36) of SCCHN. Cigarette smoking further elevated this risk to more than 20-fold (OR 23.6; 95% CI,. These data support our previous finding that suboptimal repair contributed to susceptibility to SCCHN and the new data further suggests a possible gene-environment interaction that may play an important role in the etiology of SCCHN. Further validation studies are warranted. ' 2007 Wiley-Liss, Inc.Key words: benzo[a]pyrene diol epoxide; comet assay; cancer susceptibility; gene-environment interaction; mutagen sensitivity Squamous cell carcinoma of the head and neck (SCCHN) is the 5th common cancer in the U.S. with 40,566 new patients in 2007. 1 Cigarette smoking and alcohol consumption are the known major risk factors 2 ; however, genetic factors likely play a role in SCCHN etiology, because only a fraction of those exposed to tobacco smoke develop the disease. Benzo[a]pyrene, a classic DNA-damaging carcinogen found in tobacco smoke, is metabolized by phase I enzymes to an ultimate carcinogen, benzo[a]pyrene-7,8-diol 9,10-epoxide (BPDE), which can induce DNA damage including DNA adducts through covalent binding or oxidation, leading subsequent mutations, 3,4 if not effectively repaired. It is believed that DNA repair capacity (DRC) exist to protect the DNA from mutagenic effects of exogenous and endogenous carcinogens and that inter-individual variation in DRC may contribute to cancer susceptibility. 5-7 Rare, recessive chromosomal instability syndromes, such as xeroderma pigmentosum (XP), are characterized by various defects in DNA repair and high cancer risk. 8 In addition, the capacity to repair DNA damage also varies in the general population. 9,10 Suboptimal DRC and a high level of induced DNA damage and chromosomal aberrations have been found to be associated with enhanced susceptibility to several cancers, such as those of the lung. 4,9,11 In our previously published pilot st...