Susceptibility to myasthenia gravis (MG) has been demonstrated with several HLA in different disease subgroups. HLA-DR14, -DR16 and -DQ5 were reported as predisposing factors in muscle-specific kinase antibody positive MG (MuSK-MG). These markers were evaluated in MG subgroups from Turkey. Among 164 generalized MG patients, 116 had antibodies against anti-acetylcholine receptor (AChR-MG) and 48 had MuSK-MG. Only HLA-DRB1 and DQB1 allele groups reported to be associated with MuSK-MG were compared with 250 healthy controls (HC). Highly significant associations of both DRB1(∗)16 and DRB1(∗)14 were found with MuSK-MG compared to HC (p = 1.9 × 10(-5), OR: 4.95 and p = 0.0028, OR: 3.1). On the contrary, HLA-DRB1(∗)03 was less frequent in MuSK-MG (p = 0.006, OR: 0.09). DQB1(∗)05 was also associated with MuSK-MG (p = 2.5 × 10(-6) OR: 4.8). This study provides a replication of the highly significant associations of both HLA-DRB1(∗)16,-DRB1(∗)14 and -DQB1(∗)05 with MuSK-MG. Moreover, HLA-DRB1(∗)03 appears to have a distinguishing role for this disease subgroup compared to early-onset and AChR-MG.