The FOXP3 gene encodes a transcription factor thought to be essential for the development and function of regulatory T cells, which are prevailing mediators of immunological tolerance via suppression/modulation of both T helper (Th)-1 and Th-2 mediated immune responses. Previous studies have demonstrated an association between common polymorphisms in FOXP3 and a number of immune diseases. The aim of this study was to investigate whether genetic polymorphisms at the FOXP3 locus predispose to allergic rhinitis (AR) in a Chinese Han population. Six polymorphisms in promoter and intron areas were genotyped in 193 AR subjects and 191 healthy controls. Twelve exons were also analyzed among cohorts of 157 AR patients and 118 healthy controls. Whole-population and gender strata analyses revealed that no single nucleotide polymorphisms in FOXP3 were identified as significantly associated with AR. Regarding the stratified analysis for heterozygotes and homozygotes, the heterozygous allele in rs3761548 (p = 0.020, OR(Het) = 3.12) appeared significant. Subgroup analysis for the presence of different allergen allergies also demonstrated a significant association for house dust mites (rs3060515, p = 0.010, odds ratio (OR) = 2.18; rs3761547, p = 0.013, OR = 2.00). Additionally, no polymorphisms in coding regions contributing to a susceptibility to AR were noted. Our study provides the first evidence for the association of the FOXP3 polymorphism with AR in a Chinese population.