Background: Thyroid cancer is the fifth communal cancer type in females and its occurrence rate continues to rise rapidly worldwide. Latest data demonstrated mir-125 is down-regulated in various cancer types. Methods: a case-control (179 cases, 165 controls) study in order to explore the association of mir-125 rs12976445 with the risk of thyroid cancer in the Iranian population was performed. In order to investigate rs12976445 C/T polymorphisms, polymerase chain reaction restriction–fragment length polymorphism (PCR–RFLP) was done. Logistic regression analyses were done to find the association of mir-125 rs12976445 C/T polymorphisms with thyroid cancer and its stages. Results: The genotype frequencies for patients was [(CC: 81(45.2%), CT: 75(41.9%), TT: 23 (12.9%)], and for controls was [(CC: 100 (60.1%), CT: 53(32.2%), TT: 12 (6.7%)]. The T allele distribution was significantly altered between patients and controls (P=0.002) with the odds ratio of 1.68. In the co-dominant model CC genotype was set as reference and compared with CT, and TT genotypes. In the dominant model, there was a significant difference between CC vs CT genotypes (adjusted OR = 1.69, 95% CI= 1-2.8, P = 0.026), and slightly significant differences between CC vs TT genotypes (adjusted OR = 2.18, 95% CI= 1-4.7, P = 0.047). we compared CT/TT genotype to the reference genotype (CC) and found a highly significant difference (adjusted OR = 1.78, 95% CI= 1.15-2.74, P = 0. 0.009).Conclusion: as the first study, our findings suggest that miR-125a rs12976445 is a possible prognostic biomarker for thyroid cancer patients.