Two-dimensional gel electrophoresis of immunoprecipitated human Ia-like molecules was used to investigate the structural relationship between HLA-D and HLA-DR2. Eight different lymphoblastoid lines derived from HLA-DR2-associated homozygous typing cells, representing five distinct HLA-D clusters, were compared. Two or three distinct beta chain molecules from DR-like loci were identified in the DR2 homozygous cell lines studied. Furthermore, one of these molecules was present in all lines tested, while the others were highly variable. The electrophoretic mobility of these variable DR-like molecules correlated very well with HLA-D typing studies, suggesting that the HLA-DR specificity and the HLA-D specificity on these DR2 cells may be present on separate, but related, molecules.