The HLA-DR3 haplotype is associated with increased risk of myasthenia gravis (MG) and a number of other autoimmune diseases, including insulin-dependent diabetes mellitus (IDDM), coeliac disease, and premature ovarian failure (POF). With a cDNA probe for a DQ beta gene, a 15 kb Hinc II restriction fragment has been demonstrated in genomic DNA from 7 of 16 HLA-DR3 patients with MG, 1 of 19 healthy DR3 controls, and none of 24 DR3 patients with IDDM, coeliac disease, or POF. The HLA-DQ polymorphism may be closely linked to a genetic locus regulating immune responsiveness to acetylcholine receptor and susceptibility to MG.