OBJECTIVE Moyamoya disease (MMD) is an uncommon cerebrovascular disorder, characterized by progressive occlusion at the terminal portion of the internal carotid artery. Incidence of the disease is high in East Asia and familial MMD accounts for about 15% of the disease. Although the pathogenesis is unknown, association of HLA class I or II alleles with MMD has been reported with conflicting results. We investigated whether there is a difference in HLA class II association between familial and non-familial forms of the disease. METHODS A total of 70 Korean children with MMD, including 16 familial cases (10 probands), and 207 healthy controls were studied. Among familial cases, only 10 probands were used for the HLA frequency analysis. High resolution HLA-DRB1 and DQB1 genotyping was performed using polymerase chain reaction (PCR)-sequence specific oligonucleotide hybridization and PCR-single strand conformation polymorphism methods. RESULTS The phenotype frequencies of HLA-DRB1(*)1302 (70.0%) and DQB1(*)0609 (40.0%) were significantly increased in familial MMD compared to both controls [vs. 15.5%, corrected p (p(c)) = 0.008, odds ratio (OR) = 12.76; vs. 4.3%, p(c) = 0.02, OR = 14.67] and non-familial MMD patients (vs. 14.8%, p(c) = 0.02, OR = 13.42; vs. 1.9%, p(c) = 0.02, OR = 35.33). The frequencies of DRB1 and DQB1 alleles in non-familial MMD patients were not significantly different from those in controls. CONCLUSIONS Our findings suggest that the genetic polymorphism of HLA class II genes or other closely linked disease relevant gene(s) could be a genetic predisposing factor for familial MMD.