The aim of this study was to determine the association between HLA-DQ and myasthenia gravis (MG) in 79 Swedish patients and 155 unrelated population based controls. HLA genotyping was done using polymerase chain reaction combined with sequence specific oligonucleotide probes. The DQB allele, DQB1*0201 was positively associated with MG, 39/79 (49%) patients and 43/152 (28%) controls (OR 2.47, Pc = 0.037). DQB1*0201 was observed more frequently in patients with an early onset of disease, below 30 years (Pc = 0.033). A negative association was found for DQA1*0103, 7/78 (9%) patients and 38/154 (25%) controls (OR 0.30, Pc = 0.037). DQA1*0501-DQB1*0201 and DQA1*0201-DQB1*0201 together was significantly increased in patients when compared to controls (OR 2.68; Pc = 0.019). In conclusion, two different DQ2 haplotypes (DQA1*0501-DQB1*0201 and DQA1*0201-DQB1*0201) were positively and the DQA1*0103 allele was negatively associated with MG. Susceptibility and resistance to MG in Swedish patients is mediated by HLA-DQ.