The association between myasthenia gravis (MG) and polymorphic amino acid domains in the HLA-DQ molecule was studied in 79 Swedish patients and 155 unrelated, population-based controls. A domain unique for DQB1*0201 was positively associated in MG patients with thymic hyperplasia or an early disease onset, and two domains with residues common to DQA1*01 alleles or DQB1*05 and DQB1*06 alleles were negatively associated in patients with thymic hyperplasia or an early disease onset. Our results suggest that MG associated with thymic hyperplasia and thymoma differ in their HLA-DQ association and thus are likely to have different pathogenic mechanisms.