The structural and functional heterogeneity of HLA-DR4-associated specificities was investigated in patients with seropositive juvenile rheumatoid arthritis, a DR4-associated disease. Using a combination of HLA-D analysis by mixed lymphocyte culture and electrophoretic analysis of immunoprecipitated Ia molecules by two-dimensional polyacrylamide gels, we observed a surprisingly homogeneous pattern of HLA-D antigen expression. All patients expressed common structural products of the DR and DS loci, and 7/12 homozygous DR4 patients expressed a rare and subtle HLA-D heterozygous phenotype.