Polymorphic deletions of GSTM1 and GSTT1 genes involved in the detoxification of potentially carcinogenic agents may be risk factors for various cancers, including head and neck cancer (HNC). In the present case-control study we aimed to access possible associations of HNC with GSTM1 and GSTT1 null genotypes in a Pakistani population. DNA was extracted from leukocytes of 388 cancer patients and 150 healthy controls by phenol-chloroform procedure. GSTM1 and GSTT1 deletion variants were genotyped by multiplex PCR assay with CYP1A1 as an internal control and further analyzed by primer specific PCR assay and sequencing. Mean age of cases and controls was 48 (+16.6) years with a male to female ratio of 1:1. Cancer of the oral cavity (57%) was most prevalent in the sampled population followed by pharynx and larynx (30% and 13% respectively). A statistically significant (P<0.05) association was observed for both null genotypes in contribution to HNC as compared with the controls. The odds ratio (OR) for the GSTM1 null genotype was 2.3 with a 95% CI of 1.5-5.5 and for GSTT1 OR was 2.04 with 95% CI of 1.3-3.1. These results suggest that the GSTM1 and GSTT1 null genotypes are risk factors for HNC development among the Pakistani population.