Murine splenocytes were radiolabeled with 3H- and 14C-amino acids; the Ia alloantigens encoded by the I-A and I-E/C subregions were isolated by immunoprecipitation and analyzed for structural variation by polyacrylamide gel electrophoresis. The I-A subregion products (k, d, and b haplotypes) are composed of two polypeptides, alpha and beta, with m.w. of 34,000 and 26,000 daltons, respectively. Haplotype-associated differences in m.w. were detected in the I-E/C products of the k, r, p, and d haplotypes. The alpha and beta chains of E/Ck and E/Cr are 34,000 and 28,000 daltons, respectively; E/Cp and E/Cd molecules are composed of 31,000 and 29,000 dalton polypeptides. Thus, there is both subregion (I-A vs I-E/C) and haplotype (E/Ck, E/Cr vs E/Cd, E/Cp) associated variation in the m.w. of the Ia alloantigens. Additionally, the covalent vs noncovalent association of the Ia subunits was examined and it was found that the alpha and beta chains of both I-A and I-E/C are not covalently associated. However, the I-A alpha and beta chains tend to associate through disulfide bonds during detergent lysis; the presence of alkylating agents during cell lysis prevents this association, and only free alpha and beta chains are observed under nonreducing conditions.