Genetic susceptibility to myasthenia gravis (MG) is reported frequently and varies depending on the clinical presentation of the patients. HLA-DQ genotyping was performed in 132 patients using polymerase chain reaction and sequence-specific oligonucleotide hybridizations in the Turkish population for the first time in this study. Antibody positivities against acetylcholine receptor and titin were 81 and 27%, respectively. Sixty-five percent of the patients had disease onset before 40 years of age (EOMG). Overall distribution of DQA1*0103 (odds ratio (OR): 0.5) and DQB1*0502 (OR: 1.9) alleles was different in patients and an ethnically matched healthy control group. Among the subgroups, DQB1*02 was significantly more frequent in EOMG (OR: 1.8), in women with MG (OR: 2.4), and in women with EOMG (OR: 2.8), whereas DQA1*0102 and DQB1*502 (OR: 2.3 for both) were increased and DQA1*0103 (OR: 0.04) was decreased in men with MG. Seropositivity was associated with both DQA1*03 (OR: 12.1) and DQB1*0302 (OR: 14.2) in the patient group. DQA1*02 (OR: 4.9) was associated with the presence of anti-titin antibodies, whereas DQA1*0101 (OR: 3.7) and *0102 (OR: 2.9) were more frequent in patients without this antibody. The presence of thymoma in MG was positively associated with DQB1*0301 (OR: 2.8), and DQB1*02 (OR: 0.3) was significantly less frequent in this group. The HLA-DQ associations in subgroups of MG suggest that the heterogeneity of the disease may be influenced by different genes or even by different alleles. DQ alleles have proved to be relatively informative polymorphisms in studying MG.