The extent of allelic variation of the E alpha and E beta polypeptide chains of the I-E antigens from the H-2d, H-2k, H-2p, H-2r, and H-2u haplotypes is described. E alpha and E beta chains were individually labeled with arginine or lysine and compared by tryptic peptide analysis. The results indicate minimum variability among the E alpha polypeptides encoded by the d, k, p, and r haplotypes. However, the Eu alpha chain differed significantly from the other allelic E alpha gene products. On the other hand, the E beta alleles demonstrated substantial variability with the Ed beta being notably less similar to the other alleles than they are to each other. These findings are consistent with a number of observations regarding the serology and functions of the I-E antigens.