This case-control study was carried out to investigate the possible relationship between the gene frequencies of HLA-DRB1, -DQA1 and -DQB1 alleles/haplotypes and rheumatic heart disease (RHD) among the Chinese population in Taiwan. A group of 115 patients with RHD documented by echocardiography, and a group of 115 normal controls were studied. The HLA-DRB1, -DQA1 and -DQB1 allele frequencies were determined by polymerase chain reaction and sequence-specific oligonucleotide probe. As compared with controls, patients with RHD had an increased frequency of DR11-05-DQ7 haplotype and a decreased frequency of DR4-03-DQ4 haplotype. The frequencies of DRB1, DQA1 or DQB1 alleles were not significantly different between RHD patients and controls. Further categorization of RHD patients into mitral valve disease and combined valve disease subgroups revealed no statistical difference in these alleles when compared with the two subgroups. Patients with RHD have a higher frequency of DR11-05-DQ7 haplotype and a lower frequency of DR4-03-DQ4 haplotype, which indicates that certain HLA DRB1-DQA1-DQB1 haplotypes in determining the risk/protection of RHD in Taiwan Chinese.