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Purpose: FOXP3 gene rs2232365 A/G and the rs3761548 A/C polymorphisms were associated with immune system-related diseases such as Hepatitis B virus (HBV) infection. The function of Treg cells which act as immune-suppressors in the control of HBV-related liver inflammation may be affected by these polymorphisms. The aim of the present study was to evaluate the association between these polymorphisms with HBV infection phases. Materials and Methods: The current study examined the FOXP3 gene polymorphisms in 116 patients with immune-active hepatitis B phase and in 116 individuals with inactive hepatitis B phase by a real-time polymerase chain reaction (RT-PCR). Results: In females, the A allele and AA genotype of rs2232365 polymorphism was not statistically significant although it increased 1.28- and 1.67-fold immune-active HBV risk. Although the G allele of rs2232365 polymorphism increased 1.69-fold immune active HBV risk, it was not statistically significant in males, either. Likewise, the rs3761548 polymorphism could not reach a statistically significant value in males and females, either. Conclusion: This research is to demonstrate the relation between phases of HBV infection and polymorphisms of the FOXP3 gene in the Turkish population. The results of this study showed that there is no effect of these polymorphisms on the immune-active phase of HBV, even though it increased immune-active HBV.