Crohn's disease (CD) is a chronic inflammatory bowel disease typified by transmural inflammation affecting any part of the gastrointestinal tract. CD4(+)CD25(+) regulatory T cells (T(reg) cells) play important roles in intestinal homeostasis. Adoptive transfer of regulatory T cells into mice with chronic colitis prevented inflammation and reappearance of normal intestinal architecture. The Foxp3 gene encodes a protein that is a member of the forkhead/winged-helix family of transcriptional regulators and is involved in the regulation of T cell activation. Mutation of Foxp3 gene may lead to development of autoimmune disease and inflammatory bowel disease. We investigated 10 single-nucleotide polymorphisms (SNPs) of the Foxp3 gene in CD patients and assessed allele and genotype frequencies in 93 patients with Crohn's disease (61 female and 32 male), 82 patients with primary biliary cirrhosis (PBC) (all female), and 108 normal controls (51 female and 57 male). We found that 3 SNPs (-6054, -/ATT; -3279, A/C; -924, A/G) in the promoter region and 1 SNP (IVS9+459, T/C) in the intron 9 region existed in CD patients. No significant differences of allele and genotype frequencies of all four SNPs were observed between CD patients and controls (both female and male groups). However, there was a significance difference of the comparison between PBC patients and controls in the IVS9+459 SNP. These data indicate that SNPs of the Foxp3 gene are not significantly associated with CD but are associated with PBC.