The natural resistant-associated macrophage protein 1 (NRAMP1) has been proposed as a candidate gene for the susceptibility to autoimmune diseases. In this study, the possible role of the functional polymorphism located at the promoter region of NRAMP1 gene in the susceptibility and clinical outcome of rheumatoid arthritis (RA) was investigated. A total of 141 Spanish RA patients and 194 controls previously typed for HLA-DRB1* were genotyped for the NRAMP1 polymorphism. No significant differences in the distribution of frequencies among RA patients and controls were observed. Nevertheless, when patients and controls were stratified according to their HLA shared epitope (SE) status, an increase of 2/2 genotype among SE-negative (SE-) patients with respect to SE- controls was observed (23% vs 7%, OR = 3.74, 95% CI 1.31-10.72). In addition, the possible role of this polymorphism in the clinical course of RA was investigated in a subgroup of 82 patients who were prospectively followed during a mean of 9 years. After follow-up, an increase of patients with the homozygous 2/2 genotype was detected among those with severe small joint radiological involvement: 73% of patients 2/2 had a severe form in contrast to 37% of patients with the genotype 2/3 and 30% of patients bearing 3/3 OR = 5.45, 95% CI 1.14-34.24). In conclusion, NRAMP1 gene promoter polymorphism could influence the radiological severity of rheumatoid arthritis and disease susceptibility, particularly in individuals lacking HLA-linked risk factors.