Pre-eclampsia (PE) is a multifactorial pregnancy disorder, with serious consequences for both the mother and the fetus. Despite intense studies, the pathophysiology of PE remains enigmatic. Previous studies suggested that Treg dysfunction is involved in the pathogenesis of PE. We hypothesized that functional variants of the FOXP3 gene might be associated with PE via dysregulation of Treg cells. Of the 276 subjects, we genotyped three variants of FOXP3 by PCR-RFLP and Tetra ARMS-PCR methods. The genotypic frequencies of rs2232365 were found to be protective from the development of PE under codominant [odds ratio (OR) 0.49, 95 percent confidence interval (CI) 0.28–0.87, p-value = 0.043], dominant [odds ratio (OR) 0.54, 95 percent confidence interval (CI) 0.32–0.94, p-value = 0.027] and over dominant [odds ratio (OR) 0.57, 95 percent confidence interval (CI) 0.35–0.92, p-value = 0.02] models. Moreover, the rs3761548 conferred a risk of PE in recessive model [odds ratio (OR) 2.05, 95 percent confidence interval (CI) 1.08–3.88, p-value = 0.025]. However, no mutation was detected in FOXP3 exon2 in any of the studied samples. Based on our results, thought that FOXP3 variants may be an important contributor for the progression of PE in Iranian women.