In isolating homogeneous populations of murine Ia antigens by SDS-PAGE we have found that immunoprecipitated I-Ak molecules from whole spleen possess an electrophoretically heterogeneous population of alpha-chains. SDS-PAGE of 3H-mannose-labeled I-Ak immunoprecipitates revealed that the alpha-chain peak was divided into three regions (alpha 1, alpha 2, and alpha 3), each of which migrated as a distinct individual band when isolated and reelectrophoresed. Only alpha 1 and alpha 2 labeled with 3H-fucose. Nonequilibrium pH gradient electrophoresis excluded the possibility that any of the species was invariant chain, but rather suggested that the subspecies were structurally related and that alpha 3 has fewer sialic acid residues than alpha 1 and alpha 2. Sialic acid differences between alpha 1, alpha 2, and alpha 3 were further suggested by SDS-PAGE and by peptide mapping of neuraminidase-treated immunoprecipitates. Tryptic peptide maps of 3H-leucine-labeled alpha 1, alpha 2, and alpha 3 were identical, indicating that the polypeptide backbone of the molecules is the same for all subspecies. Our results suggest that alpha 1 and alpha 2 have fucose and sialic acid and thus possess complex type oligosaccharides, whereas alpha 3 lacks these sugars and possess high mannose-type saccharides. The potential relationships of the alpha-chain subspecies is discussed. In addition, we demonstrate the usefulness of high-pressure liquid chromatography in the isolation of glycopeptides for their subsequent analysis.U