Head and neck cancer (HNC) is a serious health problem worldwide and tobacco smoke is a main causative factor for this malignancy. Interindividual genetic differences in enzymes involved in the metabolism of tobacco smoke carcinogens are one of the most important risk factors in the development of HNC. GSTM1 and GSTT1 enzymes participate in detoxifying of tobacco smoke carcinogens and have deletion polymorphisms. We performed a case control study to investigate a possible association between GSTM1 and GSTT1 variants and HNC risk. A total of 98 HNC cases, all of which were squamous cell carcinoma, and 120 healthy controls were investigated. GSTM1 and GSTT1 polymorphisms were genotyped using PCR. There was a significant association between HNC and GSTM1-null genotype (adjusted OR: 2.36, 95% CI: 1.303-4.26, p = 0.005). The frequency overall of GSTT1-null genotypes was not significant in HNC patients compared with that of GSTT1-positive genotypes (adjusted OR: 1.16, 95% CI: 0.563-2.397, p = 0.686). No combined effect was observed for GSTM1 and GSTT1 genotypes. When data were stratified by smoking status, cases having GSTM1-null genotype who were smokers conferred the highest risk (adjusted OR: 4.06, 95% CI: 1.3-12.63). Thus, our results suggest that GSTM1 polymorphism may significantly increase the risk of HNC and there is an additive interaction between GSTM1-null genotype and smoking on HNC risk.