A nine years prospective study was performed on 82 Spanish rheumatoid arthritis patients with a disease duration of less than two years at the study entry, in order to evaluate the role of HLA markers in the susceptibility and progression of rheumatoid arthritis. Radiological evaluation of disease severity was performed at the time of diagnosis and 9 years later. High resolution HLA-DR typing demonstrated that the presence of the shared epitope (SE) was more frequent among patients (61% vs. 31% in controls; p = 0.00003; OR = 3.48). Fourteen patients carried two SE+ HLA-DRB1 alleles (SE+/+); 36, one single allele (SE+/-) and 32 were SE negative (SE-/-). HLA-DR4 (particularly DRB1*0401 and DRB 1*0405) and HLA-DR10 were increased among patients. At study entry, the frequencies of locally severe (hands and feet) RA were more frequent among SE+/+ patients (79%) than among SE+/- (47%) and SE-/-(44%) patients (p = 0.05; RR = 1.80). After 9 years of disease these differences disappeared, whereas differences in the extent of the disease arise: 79%, 50% and 32% of SE+/+, SE+/- and SE-/- patients respectively showed large joints involvement (shoulders, elbows, hips and knees) (p = 0.01; RR = 2.44 for SE+/+ vs. SE-/-; and p = 0.04; RR = 1.81 for SE+ vs. SE-). These results suggest that the presence of the shared epitope is associated with the extent and progression of radiological joint damage in rheumatoid arthritis.