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 en