We have typed 64 Japanese patients with mixed connective tissue disease (MCTD) and 53 Japanese patients with systemic lupus erythematosus (SLE) for HLA-DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, and DPB1 genes by the HLA-DNA typing method using the PCR-SSOP technique. Frequencies of HLA-DRB1*0401, DRB1*0901, DRB4*0101, and DQA1*03 were increased and those of HLA-DRB1*0405 and DQB1*0401 were decreased in the patients with MCTD, while the frequencies of HLA-DRB1*1501, DRB5*0101, and DQB1*0602 were increased in the patients with SLE. The typing results suggest that susceptibility to MCTD is strongly associated with the HLA-DRB1*0401-DRB4*0101-DQA1*03-DQB1*0301 haplotype, and that to SLE is associated with the HLA-DRB1*1501-DRB5*0101-DQA1*0102-DQB1*0602 haplotype. The observation that the MCTD-associated HLA alleles are distinct from the SLE-associated ones may support the clinical entity of MCTD different from SLE.