Inflammatory bowel diseases (IBD) representing both Crohn's disease and ulcerative colitis are characterized by chronic activation of macrophages. Natural resistance-associated macrophage protein 1 (NRAMP1) gene regulates macrophage activation of antimicrobial activity and has many pleiotropic effects on macrophage functions. To explore the role of the NRAMP1 gene in IBD susceptibility, we examined the promoter sequence of the NRAMP1 gene whose polymorphisms have been reported to influence the transcriptional activity of the NRAMP1 gene. One novel allele (allele 7) and two previously reported alleles (alleles 2 and 3) have been determined in a Japanese population. We investigated the association of IBD with these three alleles. The allele frequency of allele 7 was significantly higher in patients with Crohn's disease (11.1%) and ulcerative colitis (11.2%) than those in the healthy control group (4.5%) (Pc=0.015, Pc=0.018, respectively). Therefore, our findings suggest that the novel promoter polymorphism of the NRAMP1 gene may influence susceptibility to IBD in the Japanese population.