Genome scans have identified a region spanning 40 cM on the long arm of chromosome 12 as a susceptibility locus for inflammatory bowel disease (IBD). This locus contains several candidate genes for IBD, one of which is the gene for the natural resistance associated macrophage protein 2 (NRAMP2). This protein is a divalent cation transporter and is expressed in many cells and tissues. The putative role of this protein in innate immunity prompted us to investigate a possible relationship between NRAMP2 and IBD. We assessed the frequency of four restriction fragment length polymorphisms (IVS2+11A/G, IVS4+44C/A, 1254T/C, and IVS15Ex16-16C/G) in a group of 155 Crohn's disease (CD) patients, 114 ulcerative colitis (UC) patients, and 189 healthy controls. Linkage analysis was performed in a group of 70 families with multiple members suffering from IBD. We searched for additional intragenic markers and mutations by sequence analysis of the natural resistance-associated macrophage 2 gene of 33 CD patients, with a positive family history for IBD. We identified one novel restriction fragment length polymorphism in intron 15 of the gene. The frequency of the rare allele is: 0.08 in our control population. An increased frequency of this allele was found in CD patients but this difference did not reach statistical significance. A weak association between CD and homozygosity for the G allele of the IVS2+11A/G was found (OR [odds ratio] = 2.2, CI [confidence interval] = 1.3-3.9, chi2 = 8.4, p = 1.013). Nonparametric linkage analysis and transmissions disequilibrium tests did not provide evidence for linkage of NRAMP2 to IBD, UC, or CD. Sequence analysis of the exons and the iron-responsive element in a panel of 33 CD patients did not reveal any mutations in NRAMP2. Our association, linkage, and sequence analysis in IBD shows that the putative genetic risk factor on chromosome 12 likely is not NRAMP2. The weak association between the G/G genotype of IVS2+11A/G and CD may be due to linkage disequilibrium with a nearby disease-causing gene.