Aims: To investigate the potential role of polymorphisms in matrix metalloproteinase-9 (MMP-9), glutathione S-transferase M1 (GSTM1) and T1 (GSTT1), and methylenetetrahydrofolate reductase (MTHFR) genes as risk factors for development of temporomandibular disorders (TMD) in a Serbian population. Methods: This case-control study included 282 subjects: 100 with TMD and 182 healthy controls. Genotyping was done by means of polymerase chain reaction (PCR)/restriction fragment length polymorphism (RFLP) for single nucleotide polymorphisms (SNPs) analysis (C-1562T MMP-9 and C677T MTHFR) or multiplex PCR and real-time PCR methods for deletion analysis (GSTM1, GSTT1) of DNA obtained from buccal swabs. The association of gene variants with TMD risk was determined by calculating odds ratios (OR) and their 95% confidence intervals (CI). Results: A statistically significant difference in genotype and allele frequencies was found between the TMD group and controls for the MMP-9 SNP. Heterozygotes (CT) were significantly more frequent in the TMD group than in the control group and carriers of the T allele had an approximately twofold increase of TMD risk (OR = 2.13, 95% CI = 1.24-3.67, P = .005). The null GSTT1 genotype as well as the combined non-null GSTM1/ null GSTT1 were associated with lower risk of TMD (OR = 0.28, CI = 0.10-0.74, P = .004 and OR = 0.16, CI = 0.03-0.58, P .001, respectively). GSTM1 alone and MTHFR polymorphisms did not show an association with TMD. Conclusion: The C-1562T SNP in the promoter region of the MMP-9 gene, the GSTT1 null, as well as the combined GSTM1 non-null and GSTT1 null genotypes are modulators of TMD risk in a Serbian population. Keywords: genetic polymorphisms, GSTs, MMP, MTHFR, temporomandibular disorders