The aim of this study was to compare the frequency of the HLA-DRB1 and HLA-DQB1 alleles in Korean patients with idiopathic pulmonary arterial hypertension (IPAH) and in normal controls and to determine any association that may exist between clinical characteristics of IPAH and specific HLA alleles. IPAH patients seen between October 1998 and September 2001 were retrospectively assessed, and 19 patients and 193 controls were HLA typed at the HLA-DRB1 and DQB1 loci. Clinical characteristics and hemodynamic parameters were reviewed. The patients with IPAH had a significantly higher frequency of the HLA-DRB1*0406 allele (18% vs. 6%, p = 0.004) and the HLA-DQB1*0302 allele (24% vs. 12%, p = 0.034), as well as a significantly higher frequency of haplotype DRB1*0406-DQB1*0302 (p = 0.0006). All 6 patients with haplotype DRB1*0406-DQB1*0302 (H+ group) were women, compared with 8 of the 13 patients lacking the DRB1*0406-DQB1*0302 haplotype (H- group), but without statistical significance. Three of 19 patients showed a positive short-term hemodynamic response to NO inhalation, all 3 of whom had the DRB1*0406-DQB1*0302 haplotype. There were no other significant differences in clinical characteristics and hemodynamic parameters between the H+ and H- groups. We conclude from this study that the HLA-DRB1*0406-DQB1*0302 haplotype is associated with IPAH in Korean patients. These results suggest that certain clinical characteristics of IPAH may be controlled in part by patients' HLA alleles.