We investigated polymorphisms of complement components C2, C4, and factor B (BF) in Japanese patients with rheumatoid arthritis (RA). The frequencies of C4AQ0 (32.1%) and C4B5 (35.9%) among RA patients were significantly higher than among healthy control subjects. C4B5 was strongly associated with HLA-Bw54, Bw59, DR4.1, and DQw4. C4AQ0 showed no association with HLA-Bw54 or Bw59, but there was weak association with HLA-DR4.1 and DQw4. The number of persons with both C4AQ0 and C4B5 was significantly higher in the RA patient group (relative risk 13.5). C2C and BFS were the most common alleles in RA patients, as well as in healthy control subjects. These data support the existence of 2 different putative susceptibility haplotypes (HLA-Bw54 or Bw59;C2C; BFS;C4A3;C4B5;DR4.1;DQw4 and C2C;BFS; C4AQ0;C4B1 or C4B2) in Japanese patients with RA.