Associations of GSTM1, GSTT1 and CYP1A1 gene variants with risk of developing nasopharyngeal cancer were evaluated in this case-control study, in which 130 cases along with 151 population-based healthy controls of Pashtun ethnicity from Khyber Pakhtunkhwa province of Pakistan were recruited. Socio-demographic data were obtained and blood samples were collected with informed consent for analysis. Specific RT-PCR and conventional PCR methods were used to detect CYP1A1 and GSTs, respectively, and results analyzed through SPSS version 20. Study showed that CYP1A1 homozygous (C/C) had an almost 4-fold increased risk for nasopharyngeal cancer; while heterozygous (T/C) had an almost 2 times increased risk. Overall the C allele is significantly associated with nasopharyngeal cancer as compared to T allele. Null genotypes of GSTM1 were having 3-fold increased risk; whereas null genotype of GSTT1 was having 2 times increased risk. Similarly, GSTM/GSTT both null genotype was having more than 5 times increased association. Presence of all three gene variants showed strong and significant association. Findings of the study suggest that presence of GSTM1 and/or GSTT1 null genotypes along with variant alleles of CYP1A1 are significant risk factors for nasopharyngeal cancer susceptibility in Pashtun population.