Helper T lymphocytes recognize fragments of foreign (or self) antigens in the peptide-binding clefts of major histocompatibility complex class II molecules; their activation is a crucial step in the induction of many immune and autoimmune responses. While studying the latter, we raised a T-cell line from the thymus of a myasthenia gravis patient against recombinant a subunit of the human acetylcholine receptor, the target of this autoimmune disease. The line responds to the 144-156 region of the human sequence and not to the same region of the electric fish homolog, which differs by only three residues. These CD4' T cells recognize this epitope only in the context of HLA-DR4 class II molecules, of which the variants with Gly86 are absolutely required. Thus the naturally occurring alternatives Dw14.2 (Gly56) and Dw14.1 (Val ¶*-which differ only at this one position in the entire antigen-binding region-show an all-or-nothing difference in presenting activity. This dimorphism at position 86 is widespread, occurring in subtypes of DR1, DR2, DR3, DR5, and DR6 alleles as well as DR4. Since other DR4 subtypes with substitutions at positions 70-74 also fail to present this peptide, and glycine residues can be uniquely flexible, we suggest that this replacement at position 86 acts locally or at a distance by altering the conformation of the peptide-binding cleft. Such profound functional consequences for T-cell recognition as we report here may explain this example of conserved major histocompatibility complex diversity.The striking polymorphism of the major histocompatibility complex (MHC) in most vertebrate species implies strong selection for diversity. As functional and crystallographic studies show (for class I molecules), the role of these MHC heterodimers is to bind peptide fragments of processed antigens in a cleft formed by the folding of their two membrane-distal domains (1, 2) and to present them to T lymphocytes. [For CD4' helper T cells, the class II molecules on specialized antigen-presenting cells (APCs) fulfill this role.] Specific recognition of the MHC and peptide components of the resulting composite by T lymphocytes underlies the phenomenon of MHC restriction whereby most peptides are recognized in the context of only some of the class II alleles. Thus, the diversity of the MHC molecules probably ensures that the population as a whole maintains responsiveness to a broad repertoire of foreign antigens.Many autoimmune diseases show associations with particular MHC alleles or haplotypes (reviewed in ref.3).