Graves' disease (GD) is a leading cause of hyperthyroidism, which affects 1.0-1.6% of the general population. Previous studies reported a higher GD prevalence in Asian populations compared to Caucasian populations. The etiology of GD involves complex interactions between predisposing genes and environmental triggers. Genetic studies have shown that the human leukocyte antigen (HLA) is an important candidate genetic region associated with GD in Asian populations. However, the results were inconsistent and inconclusive. Here, we performed a meta-analysis to evaluate the role of the HLA-B46 allele in GD in Asian populations. A total of 14 case-controlled studies on the association of the HLA-B46 allele in 1743 GD patients and 5689 controls were included. Our results showed a trend toward an increased risk of GD in HLA-B46-positive subjects compared to those HLA-B46-negative (OR = 2.48; 95% CI = 1.96-3.13, P < 0.01). However, there were some limitations to the current meta-analysis, such as heterogeneity (P(heterogeneity )< 0.01 and I(2 )= 68.0%) or the different typing methods (serological and genotyping methods). The meta-analysis indicated that the HLA-B46 allele is a risk factor for GD in Asian populations. Future studies on the role of the HLA-B46 allele in GD should consider complications such as periodic paralysis, ophthalmopathy and recurrence.