Background: Thyroid transcription factor gene (FOXE1) and Foxp3 play important roles in autoimmune and inflammatory disease as well as human malignancies. We aimed to investigate the association of FOXE1 and Foxp3 polymorphism with the susceptibility to differentiated thyroid cancers (DTC). Methods: Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 350 DTC patients and 306 healthy controls. Results: AA/AG genotype of FOXE1-rs1867277 and AA/AC genotype of Foxp3-rs3761548 were associated with a higher risk of DTC. The frequency of Foxp3-rs2280883 CC/CT genotype was lower in DTC patients. Besides, the AA/AC genotype of rs3761548 was more frequent in female DTC than the male. We further analyzed the association between 3 single nucleotide polymorphisms (SNPs) and DTC. We found that rs3761548 AA/AC genotype was more frequent in severe DTC patients (tumor diameter >1 cm) compared with the relative tender DTC patients (tumor diameter <1 cm). On the contrast, the frequency of rs2280883 CC/CT genotype was lower in severe DTC patients. Conclusion: Our findings suggested that FOXE1 and Foxp3 polymorphism were associated with the risk of DTC in Chinese Han population. Besides, rs3761548 AA/CC genotype was a potential risk factor for the susceptibility to DTC and rs2280883 CC/CT was a protective factor.