Background: There is increasing evidence for the role of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatic amines (HCAs) in carcinogenesis, including oral squamous cell carcinoma (OSCC). Several of these mutagenic substances are cytochrome (CYP)2C9 enzyme substrates.Methods: In this study, we examined the association of CYP2C9*2 and *3 genetic polymorphisms in 58 OSCC patients and 174 healthy, age, and sex-matched controls. Genotyping was done with allele-specific polymerase chain reaction followed by agarose gel electrophoreses, while selected samples were sequenced for confirmation of genotyping.Results: The wild type genotype (CYP2C9*1*1) was observed at 83%, *1*3 at 8%, *1*2 at 5%, *2*2 at 2% and *2*3 at 2% in combined case and control groups. On further analysis, however, our results did not reveal an association of these variants with OSCC samples (Odds ratio: 0.608, 95% Confidence Interval: 0.289 - 1.281, p-value: 0.190). While larger studies are needed to confirm or refute these results, they show a lack of association of CYP2C9*2 and *3 polymorphisms with OSCC in this population.Conclusions: This study demonstrates that the genetic polymorphisms in CYP2C9 genes (CYP2C9*2 and *3) are not causing the risk and are not associated with OSCC. Also, CYP2C9 has no role in the pathogenesis of OSCC in this population of patients.Trial registration: Not applicable.