We investigated the effect of different levels of smoking and drinking on the development of squamous cell carcinoma of head and neck (HNSCC) and performed analyses to evaluate possible differences in cancer susceptibility among the anatomical subregions of head and neck. Moreover, we investigated the association between 5 single nucleotide polymorphisms (SNPs) in the homologous recombination DNA repair pathway (XRCC3 c.-1843 A>G, XRCC3 c.562-14 A>G, XRCC3 c.722 C>T, Rad51 c.-3429 G>C, Rad51 c.-3392 G>T) and 4 SNPs in the non- homologous end joining DNA repair pathway (Lig4 c.26 C>T, Lig4 c.1704 T>C, Ku70 c.-1310 C>G and Ku80 c.2110-2408 G>A) on one hand and the risk of the development of HNSCC on the other hand in a case- control setting in a Caucasian population. The study population consisted out of 152 HNSCC patients and 157 healthy controls, matched for age and gender. Polymorphic regions were analysed using the PCR-RFLP and PCR-single base extension assays. Stratification of the populations according to smoking habits and alcohol consumption highlighted the importance of tobacco and alcohol as two risk factors for the development of HNSCC (OR=11.81, p<0.01 and OR=4.66, p<0.01 for high exposure to tobacco and alcohol respectively). A stratification according to the anatomical region of the tumour showed site specific differences in sensitivity to tobacco smoke, with an increase in cancer susceptibility from the oral cavity down to the pharynx and larynx (OR=6.86, p<0.01; OR=9.83, p<0.01 and 36.57, p<0.01 for >25PY). A significant positive association between the XRCC3 c.722 polymorphism and HNSCC was found, with an adjusted odds ratio (OR) of 1.96 (p=0.02). Both the Lig4 c.26 and the Rad51 c.-3429 polymorphisms were associated with a significant reduced risk for HNSCC (OR=0.43, p=0.01; OR=0.43, p=0.05 respectively). Analysis of the gene- smoking interaction revealed no differences in OR for XRCC3 c.722 among the smoking groups. The protective effect seen for the Rad51 c.-3429 and polymorphism was most prominent among the group of heavy smokers (>25 PY). No associations with risk for HNSCC were found for the other SNPs in genes of the DNA DSB repair pathways.