Monoclonal antibodies directed against nonpolymorphic determinants of HLA-D/DR molecular complex (human Ia antigens) were used to immunoprecipitate HLA-D-region-associated molecules from [35S]methionine internally labeled and 125I surface-labeled B lymphoblastoid B cell lines. Analysis of these by two-dimensional nonequilibrium-pH-gradient electrophoresis reveals a molecular heterogeneity within a 26,000- to 34,000-mol wt range. At least three sets of spots are identified: a very acidic set of 32,000- to 34,000-mol wt, a very intense invariant spot of 31,000 mol wt, and a series of 26,000- to 29,000-mol wt spots of variable charge. Comparison of immunoprecipitates from nine different HTC demonstrates that the polymorphism is localized in this latter set. Pulse-labeling and inhibition of glycosylation by tunicamycin show that the electrophoretic polymorphism is of polypeptide origin, whereas N-linked oligosaccharrides and sialic acid residues contribute to the microheterogeneity of the profile. Two-dimensional gels provide an electrophoretic genotyping procedure and allow analysis of the genetic organization and molecular complexity of the HLA-D/DR molecules.