Several products of the I region of the mouse H-2 complex have been characterized by micropeptide analysis, microsequence analysis, and two-dimensional gel (IEF/SDS-PAGE) analysis. Ia antigens have been isolated using the biosynthetic radiolabeling technique together with highly specific alloantisera and indirect immunoprecipitation. Chromatography of tryptic peptides prepared from the α and β polypeptides of Ia antigens encoded by the I-A and I-EC subregions will be compared from both spleen and epidermal cell preparations. These data, in conjunction with partial N-terminal amino acid sequence data on Ia antigens from the I-Ab, I-Ak, I-Ad, I-As, I-ECk and I-ECd subregions and haplotypes will be discussed in terms of homology relationships and haplotype-associated differences in the structures of these Ia polypeptides. Two-dimensional gel patterns of isolated α and β polypeptides will also be presented. The implications of these data will be discussed as they relate to the genetic organization of the I-region.