Genetic analyses indicate that HIA complex genes can be involved in susceptibility to autoimmune myasthenia gravis (MG). Various HLA alleles serve as genetic elements that either predispose to or protect against MG. This study investigates the probable relationship between HLA-DQ allele polymorphisms and MG cases in northern China. The HLA-DQA1 and DQB1 alleles were determined by polymerase chain reaction/sequence-specific primers (PCR-SSP) in 84 MG patients, and the results were compared to 293 healthy controls. Our findings indicate that DQA1*0401(P = 0.008, OR: 2.5, 95%CI: 1.24-3.07) and B1*0301(P = 0.000, OR: 2.29, 95%CI: 1.48-3.54) were the most frequent allele; the frequencies of DQA1*0103(P = 0.000, OR:0.24, 95%CI 0.13-0.49) and DQB1*0601(P = 0.001, OR:0.40, 95%CI 022-0.50) were significantly decreased in MG patients compared with healthy controls. Patients with thymomatous MG were positively associated with DQA1 *0401(P = 0.011, OR:4.57, 95% CI 1.40-14.90) and DQB1 *0604 (P = 0.001, OR: 4.01,95% CI 1.65-9.73) as compared to MG patients without thymoma. Different genetic mechanisms may exist between MG patients with thymoma and those without thymoma. The HLA-DQ associations in MG subgroups suggest that disease heterogeneity may be influenced by different genes or alleles. Crown Copyright (C) 2011 Published by Elsevier B.V. All rights reserved.