Ia antigens are polymorphic cell-surface glycoprotein complexes, encoded within the I region of the mouse major histocompatibility complex, that control the ability of the organism to mount effective antigen-specific immune responses. We have isolated and determined the nucleotide sequences of cDNA and genomic clones for the I-Eβ sgene and we present the predicted protein sequence for most of the Eβ spolypeptide chain. The Eβ spolypeptide shows 95% protein homology to the other cloned Eβalleles. Comparison of the protein sequences of five Eβalleles from haplotypes that differ in responder phenotype to pigeon cytochrome c suggests that the structure of one of the Eβhypervariable regions may determine responsiveness to this antigen.