Objective To investigate the relationship between forkhead/winged helix transcription factor (Foxp) 3 gene polymorphisms and susceptibility and phenotype of Crohn's disease (CD) in Han nationality in Zhejiang province.Methods From January 2007 to December 2015,268 diagnosed CD patients and 490 healthy controls were enrolled.The four single nucleotide polymorphism (SNP) of Foxp3 rs3761547,rs2232365,rs2294021 and rs3761548 were examined by a SNaPshot technique,and their relation with the efficacy of infliximab was evaluated.The linkage disequilibrium (LD) and haplotype were also analyzed.Unconditional Logistic regression analysis was performed for statistical analysis.Results There was no significant difference in the four mutant alleles and genotype frequencies between 31 patients with effective infliximab treatment and 19 patients with ineffective treatment (all P＞0.05).The results of LD analysis indicated that the above four SNP were in a tight linkage.The frequency of haplotype GCGC of male CD group was 29.20％ (40/137),which was higher than that of male healthy control group (19.37％,43/222),and the difference was statistically significant (odd ratio (OR)=1.717,95％ confidence interval (CI) 1.045 to 2.820,P=0.032).The frequency of haplotype ACGA of female CD group was 13.36％ (35/262),which was lower than that of female healthy control group (19.03％,102/536),and the difference was statistically significant (OR=0.656,95％CI 0.433 to 0.995,P=0.046).The frequency of haplotype ATAC of male colon (L2) type was 25.93％ (7/27),which was lower than that of ileocecal colon (L3) type (75.38％,49/65),and the difference was statistically significant (OR=0.114,95％CI 0.041 to 0.320,P＜0.01).The frequency of haplotype GCGC of male L2 type was 51.85％ (14/27),which was higher than that of L3 type (9.23％,6/65),and the difference was statistically significant (OR=10.590,95％CI 3.423 to 32.758,P＜0.01).The frequency of haplotype ATAC of male stenotic (B2) type was 73.21％ (41/56),which was higher than that of nonstenotic and nonpenetrated (B1) type (47.30％,35/74),and the difference was statistically significant (OR=0.328,95％CI 0.156 to 0.693,P=0.003).The frequency of haplotype GCGC of male B2 type was 17.86％ (10/56) which was lower than that of nonstenotic and nonpenetrated (B1) type (39.19％,29/74),and the difference was statistically significant (OR=2.946,95％CI 1.295 to 6.784,P=0.009).The frequency of haplotype ACGA of male penetrated (B3) type was 71.43％ (5/7),which was higher than that of nonstenotic and nonpenetrated (B1) type (12.16％,9/74),and the difference was statistically significant (OR =0.055,95％ CI 0.009 to 0.329,P ＜ 0.01).Conclusion Foxp3 (rs3761547,rs2232365,rs2294021,rs3761548) gene polymorphisms are associated with the susceptibility and phenotype of CD in Chinese Han patients,but not related with the efficacy of infliximab.